+ exec
+ rm -rf /rpmbuild
+ mkdir -p /rpmbuild
+ su -c 'rpmbuild -ba /builddir/build/SPECS/bowtie.spec            --define "debug_package %{nil}"            --undefine _annotated_build            --define "_missing_doc_files_terminate_build %{nil}"            --define "_emacs_sitestartdir /usr/share/emacs/site-lisp/site-start.d"            --define "_emacs_sitelispdir /usr/share/emacs/site-lisp"            --nocheck   ' mockbuild
warning: Macro expanded in comment on line 12: %{name}-script-shebang.patch

warning: Macro expanded in comment on line 13: %{name}-gcc47.patch

Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.sHXf1T
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf bowtie-1.0.1
+ /usr/bin/unzip -qq /builddir/build/SOURCES/bowtie-1.0.1-src.zip
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd bowtie-1.0.1
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ echo 'Patch #0 (bowtie-arm-gcc.patch):'
Patch #0 (bowtie-arm-gcc.patch):
+ /usr/bin/patch --no-backup-if-mismatch -p1 -b --suffix .bowtie-arm-gcc.patch --fuzz=0
patching file Makefile
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.xkvDrf
+ umask 022
+ cd /builddir/build/BUILD
+ cd bowtie-1.0.1
+ make -j4 -p 'EXTRA_FLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 '
g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1   \"" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1     \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \
	-I SeqAn-1.1 -I third_party \
	-o bowtie-build ebwt_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp  bowtie_build_main.cpp \
	-lpthread 
g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1   \"" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1    \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \
	-I SeqAn-1.1 -I third_party \
	-o bowtie ebwt_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
	-lpthread 
g++ -O3 \
	-DCOMPILER_OPTIONS="\"-O3 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1   \"" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1    \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall \
	-I SeqAn-1.1 -I third_party -I . \
	-o bowtie-inspect bowtie_inspect.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp \
	-lpthread
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from SeqAn-1.1/seqan/find.h:31,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from SeqAn-1.1/seqan/find.h:31,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^~~~~~~~~
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^~~
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^~~~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^~~
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^~~~~~~~~
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/find.h:62:0,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function 'void seqan::_patternInit(seqan::Pattern<TNeedle, seqan::Tag<seqan::_MultipleShiftAnd> >&)':
SeqAn-1.1/seqan/find/find_multiple_shiftand.h:220:23: warning: typedef 'TWord' locally defined but not used [-Wunused-local-typedefs]
  typedef unsigned int TWord;
                       ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^~~
In file included from SeqAn-1.1/seqan/find.h:62:0,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function 'void seqan::_patternInit(seqan::Pattern<TNeedle, seqan::Tag<seqan::_MultipleShiftAnd> >&)':
SeqAn-1.1/seqan/find/find_multiple_shiftand.h:220:23: warning: typedef 'TWord' locally defined but not used [-Wunused-local-typedefs]
  typedef unsigned int TWord;
                       ^~~~~
In file included from SeqAn-1.1/seqan/index.h:82:0,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0> >&, TIter)':
SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
                                                              ^~~~~~~
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, TIter)':
SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
                                                                 ^~~~~~~
SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
                                                                ^~~~~
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^~~~~~~
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^~~~~~~
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^~~~~~~
In file included from SeqAn-1.1/seqan/index.h:83:0,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, TIter)':
SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
                                                              ^~~~~~~
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
                                                                           ^~~~~~~
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
                                                                           ^~~~~~~
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from ebwt_search.cpp:11:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^~~~~~~~~
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from ebwt_search.cpp:11:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from ebwt_build.cpp:7:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^~~~~~~~~
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from ebwt_build.cpp:7:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
In file included from SeqAn-1.1/seqan/index.h:82:0,
                 from ebwt.h:16,
                 from bowtie_inspect.cpp:10:
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0> >&, TIter)':
SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
                                                              ^~~~~~~
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, TIter)':
SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
                                                                 ^~~~~~~
SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
                                                                ^~~~~
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^~~~~~~
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^~~~~~~
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^~~~~~~
In file included from SeqAn-1.1/seqan/index.h:83:0,
                 from ebwt.h:16,
                 from bowtie_inspect.cpp:10:
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, TIter)':
SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
                                                              ^~~~~~~
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
                                                                           ^~~~~~~
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
                                                                           ^~~~~~~
In file included from SeqAn-1.1/seqan/index.h:82:0,
                 from ebwt.h:16,
                 from ebwt_search.cpp:14:
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0> >&, TIter)':
SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
                                                              ^~~~~~~
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, TIter)':
SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
                                                                 ^~~~~~~
SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
                                                                ^~~~~
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^~~~~~~
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^~~~~~~
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^~~~~~~
In file included from SeqAn-1.1/seqan/index.h:83:0,
                 from ebwt.h:16,
                 from ebwt_search.cpp:14:
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, TIter)':
SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
                                                              ^~~~~~~
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
                                                                           ^~~~~~~
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
                                                                           ^~~~~~~
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from ebwt.h:24,
                 from bowtie_inspect.cpp:10:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^~~~~~~~~
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from ebwt.h:24,
                 from bowtie_inspect.cpp:10:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
In file included from blockwise_sa.h:13:0,
                 from ebwt.h:27,
                 from ebwt_build.cpp:11:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:156:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:156:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:157:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:157:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
In file included from blockwise_sa.h:13:0,
                 from ebwt.h:27,
                 from ebwt_search.cpp:14:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:156:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:156:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:157:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:157:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
In file included from ebwt.h:27:0,
                 from ebwt_build.cpp:11:
blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA<TStr>::~KarkkainenBlockwiseSA()':
blockwise_sa.h:206:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
   if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample
   ^~
blockwise_sa.h:206:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
   if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample
                               ^~~
In file included from ebwt.h:27:0,
                 from ebwt_search.cpp:14:
blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA<TStr>::~KarkkainenBlockwiseSA()':
blockwise_sa.h:206:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
   if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample
   ^~
blockwise_sa.h:206:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
   if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample
                               ^~~
blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()':
blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TStr>::Type TAlphabet;
                                     ^~~~~~~~~
blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()':
blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TStr>::Type TAlphabet;
                                     ^~~~~~~~~
blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()':
blockwise_sa.h:745:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TStr>::Type TAlphabet;
                                     ^~~~~~~~~
blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()':
blockwise_sa.h:745:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TStr>::Type TAlphabet;
                                     ^~~~~~~~~
In file included from ebwt_build.cpp:11:0:
ebwt.h: In destructor 'Ebwt<TStr>::~Ebwt()':
ebwt.h:802:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_fchr    != NULL) delete[] _fchr;    _fchr    = NULL;
    ^~
ebwt.h:802:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_fchr    != NULL) delete[] _fchr;    _fchr    = NULL;
                                            ^~~~~
ebwt.h:803:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_ftab    != NULL) delete[] _ftab;    _ftab    = NULL;
    ^~
ebwt.h:803:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_ftab    != NULL) delete[] _ftab;    _ftab    = NULL;
                                            ^~~~~
ebwt.h:804:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_eftab   != NULL) delete[] _eftab;   _eftab   = NULL;
    ^~
ebwt.h:804:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_eftab   != NULL) delete[] _eftab;   _eftab   = NULL;
                                            ^~~~~~
ebwt.h:810:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_isa     != NULL) delete[] _isa;     _isa     = NULL;
    ^~
ebwt.h:810:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_isa     != NULL) delete[] _isa;     _isa     = NULL;
                                            ^~~~
ebwt.h:811:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_plen    != NULL) delete[] _plen;    _plen    = NULL;
    ^~
ebwt.h:811:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_plen    != NULL) delete[] _plen;    _plen    = NULL;
                                            ^~~~~
In file included from ebwt_search.cpp:14:0:
ebwt.h: In destructor 'Ebwt<TStr>::~Ebwt()':
ebwt.h:802:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_fchr    != NULL) delete[] _fchr;    _fchr    = NULL;
    ^~
ebwt.h:802:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_fchr    != NULL) delete[] _fchr;    _fchr    = NULL;
                                            ^~~~~
ebwt.h:803:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_ftab    != NULL) delete[] _ftab;    _ftab    = NULL;
    ^~
ebwt.h:803:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_ftab    != NULL) delete[] _ftab;    _ftab    = NULL;
                                            ^~~~~
ebwt.h:804:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_eftab   != NULL) delete[] _eftab;   _eftab   = NULL;
    ^~
ebwt.h:804:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_eftab   != NULL) delete[] _eftab;   _eftab   = NULL;
                                            ^~~~~~
ebwt.h:812:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL;
    ^~
ebwt.h:812:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL;
                                            ^~~~~~~~
ebwt.h:810:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_isa     != NULL) delete[] _isa;     _isa     = NULL;
    ^~
ebwt.h:810:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_isa     != NULL) delete[] _isa;     _isa     = NULL;
                                            ^~~~
ebwt.h:811:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_plen    != NULL) delete[] _plen;    _plen    = NULL;
    ^~
ebwt.h:811:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_plen    != NULL) delete[] _plen;    _plen    = NULL;
                                            ^~~~~
ebwt.h:812:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL;
    ^~
ebwt.h:812:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL;
                                            ^~~~~~~~
In file included from blockwise_sa.h:13:0,
                 from ebwt.h:27,
                 from bowtie_inspect.cpp:10:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:156:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:156:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:157:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:157:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
In file included from ebwt.h:27:0,
                 from bowtie_inspect.cpp:10:
blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA<TStr>::~KarkkainenBlockwiseSA()':
blockwise_sa.h:206:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
   if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample
   ^~
blockwise_sa.h:206:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
   if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample
                               ^~~
blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()':
blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TStr>::Type TAlphabet;
                                     ^~~~~~~~~
blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()':
blockwise_sa.h:745:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TStr>::Type TAlphabet;
                                     ^~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
SeqAn-1.1/seqan/sequence/string_packed.h:906:43:   required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]'
SeqAn-1.1/seqan/sequence/string_packed.h:1237:17:   required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]'
SeqAn-1.1/seqan/sequence/string_base.h:181:29:   required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::Type = long unsigned int]'
blockwise_sa.h:354:42:   required from here
SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<unnamed>' and 'enum seqan::BitsPerValue<unsigned int>::<unnamed>' [-Wenum-compare]
   VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE),
                     ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
SeqAn-1.1/seqan/sequence/string_packed.h:731:75:   required from 'typename seqan::Size<seqan::String<TValue, seqan::Packed<THostspec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Alloc<void>; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, seqan::Packed<THostspec> > >::Type = long unsigned int]'
ebwt.h:4022:9:   required from 'static TStr Ebwt<TStr>::join(std::vector<FileBuf*>&, std::vector<RefRecord>&, uint32_t, const RefReadInParams&, uint32_t) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; uint32_t = unsigned int]'
ebwt_build.cpp:453:36:   required from 'void driver(const string&, std::vector<std::__cxx11::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; std::__cxx11::string = std::__cxx11::basic_string<char>]'
ebwt_build.cpp:595:69:   required from here
SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<unnamed>' and 'enum seqan::BitsPerValue<unsigned int>::<unnamed>' [-Wenum-compare]
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
SeqAn-1.1/seqan/sequence/string_packed.h:906:43:   required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]'
SeqAn-1.1/seqan/sequence/string_packed.h:1237:17:   required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]'
SeqAn-1.1/seqan/sequence/string_base.h:181:29:   required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::Type = long unsigned int]'
blockwise_sa.h:354:42:   required from here
SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<unnamed>' and 'enum seqan::BitsPerValue<unsigned int>::<unnamed>' [-Wenum-compare]
   VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE),
                     ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
In file included from bowtie_inspect.cpp:10:0:
ebwt.h: In destructor 'Ebwt<TStr>::~Ebwt()':
ebwt.h:802:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_fchr    != NULL) delete[] _fchr;    _fchr    = NULL;
    ^~
ebwt.h:802:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_fchr    != NULL) delete[] _fchr;    _fchr    = NULL;
                                            ^~~~~
ebwt.h:803:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_ftab    != NULL) delete[] _ftab;    _ftab    = NULL;
    ^~
ebwt.h:803:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_ftab    != NULL) delete[] _ftab;    _ftab    = NULL;
                                            ^~~~~
ebwt.h:804:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_eftab   != NULL) delete[] _eftab;   _eftab   = NULL;
    ^~
ebwt.h:804:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_eftab   != NULL) delete[] _eftab;   _eftab   = NULL;
                                            ^~~~~~
ebwt.h:810:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_isa     != NULL) delete[] _isa;     _isa     = NULL;
    ^~
ebwt.h:810:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_isa     != NULL) delete[] _isa;     _isa     = NULL;
                                            ^~~~
ebwt.h:811:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_plen    != NULL) delete[] _plen;    _plen    = NULL;
    ^~
ebwt.h:811:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_plen    != NULL) delete[] _plen;    _plen    = NULL;
                                            ^~~~~
ebwt.h:812:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL;
    ^~
ebwt.h:812:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL;
                                            ^~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
SeqAn-1.1/seqan/sequence/string_packed.h:906:43:   required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]'
SeqAn-1.1/seqan/sequence/string_packed.h:1237:17:   required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]'
SeqAn-1.1/seqan/sequence/string_base.h:181:29:   required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::Type = long unsigned int]'
blockwise_sa.h:354:42:   required from here
SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<unnamed>' and 'enum seqan::BitsPerValue<unsigned int>::<unnamed>' [-Wenum-compare]
   VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE),
                     ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
SeqAn-1.1/seqan/sequence/string_packed.h:509:6:   required from 'typename seqan::Size<const seqan::String<TValue, seqan::Packed<THostspec> > >::Type seqan::capacity(const seqan::String<TValue, seqan::Packed<THostspec> >&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; THostspec = seqan::Alloc<void>; typename seqan::Size<const seqan::String<TValue, seqan::Packed<THostspec> > >::Type = long unsigned int]'
SeqAn-1.1/seqan/sequence/string_base.h:1429:49:   required from 'static typename seqan::Size<T>::Type seqan::_Resize_String<TExpand>::resize_(T&, typename seqan::Size<T>::Type) [with T = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; TExpand = const seqan::Tag<seqan::TagExact_>; typename seqan::Size<T>::Type = long unsigned int]'
SeqAn-1.1/seqan/sequence/string_base.h:1459:52:   required from 'typename seqan::Size<seqan::String<TValue, TSpec> >::Type seqan::resize(seqan::String<TValue, TSpec>&, TSize, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, TSpec> >::Type = long unsigned int]'
ebwt.h:2938:8:   required from 'void Ebwt<TStr>::restore(TStr&) const [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >]'
bowtie_inspect.cpp:267:2:   required from 'void print_index_sequences(std::ostream&, Ebwt<TStr>&, const BitPairReference&) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; std::ostream = std::basic_ostream<char>]'
bowtie_inspect.cpp:445:42:   required from here
SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<unnamed>' and 'enum seqan::BitsPerValue<unsigned int>::<unnamed>' [-Wenum-compare]
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^~~~~~~~~
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^~~
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from ref_read.h:12,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^~~~~~~~~
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from ref_read.h:12,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^~~~~~~~~
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^~~
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from ref_read.h:12,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^~~~~~~~~
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from ref_read.h:12,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^~~~~~~~~
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^~~
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from ref_read.h:12,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^~~~~~~~~
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from ref_read.h:12,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from pat.cpp:5:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from pat.cpp:5:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from pat.cpp:5:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from pat.cpp:5:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from pat.cpp:5:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^~~~~~~~~
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from pat.cpp:5:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^~~
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from pat.cpp:6:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^~~~~~~~~
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from pat.cpp:6:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from ebwt_search_util.h:8,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from ebwt_search_util.h:8,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from ebwt_search_util.h:8,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from ebwt_search_util.h:8,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from ebwt_search_util.h:8,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^~~~~~~~~
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from ebwt_search_util.h:8,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^~~
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from hit.h:12,
                 from ebwt_search_util.h:9,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^~~~~~~~~
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from hit.h:12,
                 from ebwt_search_util.h:9,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from hit_set.cpp:10:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from hit_set.cpp:10:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from hit_set.cpp:10:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from hit_set.cpp:10:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from hit_set.cpp:10:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^~~~~~~~~
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from hit_set.cpp:10:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^~~
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from hit_set.cpp:11:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^~~~~~~~~
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from hit_set.cpp:11:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from pat.h:12,
                 from sam.cpp:11:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from pat.h:12,
                 from sam.cpp:11:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from pat.h:12,
                 from sam.cpp:11:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from pat.h:12,
                 from sam.cpp:11:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from pat.h:12,
                 from sam.cpp:11:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^~~~~~~~~
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from pat.h:12,
                 from sam.cpp:11:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^~~
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from pat.h:13,
                 from sam.cpp:11:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^~~~~~~~~
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from pat.h:13,
                 from sam.cpp:11:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from alphabet.h:6,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from alphabet.h:6,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from alphabet.h:6,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from alphabet.h:6,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from alphabet.h:6,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^~~~~~~~~
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from alphabet.h:6,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^~~
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^~~~~~~~~
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from hit.h:11,
                 from hit.cpp:1:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from hit.h:11,
                 from hit.cpp:1:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^~~~~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from hit.h:11,
                 from hit.cpp:1:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from hit.h:11,
                 from hit.cpp:1:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from hit.h:11,
                 from hit.cpp:1:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^~~~~~~~~
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from hit.h:11,
                 from hit.cpp:1:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^~~
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from hit.h:12,
                 from hit.cpp:1:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^~~~~~~~~
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from hit.h:12,
                 from hit.cpp:1:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
# GNU Make 4.2.1
# Built for riscv64-unknown-linux-gnu
# Copyright (C) 1988-2016 Free Software Foundation, Inc.
# License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
# This is free software: you are free to change and redistribute it.
# There is NO WARRANTY, to the extent permitted by law.

# Make data base, printed on Fri Feb 23 20:29:57 2018

# Variables

# automatic
<D = $(patsubst %/,%,$(dir $<))
# default
COMPILE.m = $(OBJC) $(OBJCFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -c
# automatic
?F = $(notdir $?)
# makefile (from 'Makefile', line 16)
EXTRA_CXXFLAGS = 
# default
.SHELLFLAGS := -c
# makefile (from 'Makefile', line 139)
RELEASE_FLAGS = -O3
# makefile (from 'Makefile', line 88)
OTHER_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp
# environment
RPM_DOC_DIR = /usr/share/doc
# makefile (from 'Makefile', line 76)
PREF_DEF = -DPREFETCH_LOCALITY=$(PREFETCH_LOCALITY)
# default
CWEAVE = cweave
# environment
RPM_BUILD_DIR = /builddir/build/BUILD
# makefile (from 'Makefile', line 6)
SEQAN_INC = -I $(SEQAN_DIR)
# makefile (from 'Makefile', line 189)
DEFS = -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" $(FILE_FLAGS) $(PTHREAD_DEF) $(PREF_DEF) $(MM_DEF) $(SHMEM_DEF)
# automatic
@D = $(patsubst %/,%,$(dir $@))
# automatic
@F = $(notdir $@)
# default
MAKE_VERSION := 4.2.1
# makefile
CURDIR := /builddir/build/BUILD/bowtie-1.0.1
# makefile
SHELL = /bin/sh
# environment
CONFIG_SITE = NONE
# makefile (from 'Makefile', line 22)
CYGWIN = 0
# default
CO = co
# makefile (from 'Makefile', line 40)
MACOS = 0
# environment
JOURNAL_STREAM = 7:2917
# default
PREPROCESS.F = $(FC) $(FFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -F
# automatic
?D = $(patsubst %/,%,$(dir $?))
# default
LINK.m = $(OBJC) $(OBJCFLAGS) $(CPPFLAGS) $(LDFLAGS) $(TARGET_ARCH)
# default
LINK.o = $(CC) $(LDFLAGS) $(TARGET_ARCH)
# default
OUTPUT_OPTION = -o $@
# environment
RPM_LD_FLAGS = -Wl,-z,relro  -specs=/usr/lib/rpm/redhat/redhat-hardened-ld
# default
COMPILE.cpp = $(COMPILE.cc)
# makefile (from 'Makefile', line 1)
MAKEFILE_LIST :=  Makefile
# makefile (from 'Makefile', line 201)
DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(ALL_FLAGS)\""
# makefile (from 'Makefile', line 57)
SHMEM_DEF = -DBOWTIE_SHARED_MEM
# 'override' directive
GNUMAKEFLAGS := 
# default
LINK.p = $(PC) $(PFLAGS) $(CPPFLAGS) $(LDFLAGS) $(TARGET_ARCH)
# makefile (from 'Makefile', line 18)
CXXFLAGS = $(EXTRA_CXXFLAGS)
# environment
DBUS_SESSION_BUS_ADDRESS = unix:path=/run/user/1000/bus
# makefile (from 'Makefile', line 99)
VERSION = $(shell cat VERSION)
# makefile (from 'Makefile', line 10)
CC = gcc
# environment
_ = /usr/bin/make
# default
CHECKOUT,v = +$(if $(wildcard $@),,$(CO) $(COFLAGS) $< $@)
# environment
RPM_SOURCE_DIR = /builddir/build/SOURCES
# makefile (from 'Makefile', line 23)
MINGW = 0
# makefile (from 'Makefile', line 67)
PTHREAD_LIB = -lpthread
# makefile (from 'Makefile', line 8)
CPP = g++
# default
LINK.cc = $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) $(TARGET_ARCH)
# makefile (from 'Makefile', line 98)
SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
# makefile (from 'Makefile', line 61)
PTHREAD_DEF = 
# default
MAKE_HOST := riscv64-unknown-linux-gnu
# environment
PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin
# environment
RPM_OPT_FLAGS = -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 
# makefile (from 'Makefile', line 79)
SEARCH_LIBS = 
# default
TEXI2DVI = texi2dvi
# default
YACC = yacc
# default
COMPILE.mod = $(M2C) $(M2FLAGS) $(MODFLAGS) $(TARGET_ARCH)
# environment
XDG_RUNTIME_DIR = /run/user/1000
# makefile (from 'Makefile', line 17)
CFLAGS = $(EXTRA_CFLAGS)
# default
ARFLAGS = rv
# default
LINK.r = $(FC) $(FFLAGS) $(RFLAGS) $(LDFLAGS) $(TARGET_ARCH)
# default
LINT = lint
# makefile (from 'Makefile', line 140)
NOASSERT_FLAGS = -DNDEBUG
# default
COMPILE.f = $(FC) $(FFLAGS) $(TARGET_ARCH) -c
# default
LINT.c = $(LINT) $(LINTFLAGS) $(CPPFLAGS) $(TARGET_ARCH)
# default
YACC.m = $(YACC) $(YFLAGS)
# default
YACC.y = $(YACC) $(YFLAGS)
# default
AR = ar
# makefile (from 'Makefile', line 95)
BUILD_CPPS = 
# environment
INVOCATION_ID = d28b954697334133a4ddf46d47eff855
# default
.FEATURES := target-specific order-only second-expansion else-if shortest-stem undefine oneshell archives jobserver output-sync check-symlink load
# makefile (from 'Makefile', line 21)
WINDOWS = 0
# default
TANGLE = tangle
# default
GET = get
# automatic
%F = $(notdir $%)
# makefile (from 'Makefile', line 171)
SRC_PKG_LIST = $(wildcard *.h) $(wildcard *.hh) $(wildcard *.c) $(wildcard *.cpp) $(wildcard third_party/*.h) $(wildcard third_party/*.hh) $(wildcard third_party/*.c) $(wildcard third_party/*.cpp) doc/strip_markdown.pl Makefile $(GENERAL_LIST)
# default
COMPILE.F = $(FC) $(FFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -c
# default
CTANGLE = ctangle
# makefile (from 'Makefile', line 183)
BIN_PKG_LIST = $(GENERAL_LIST)
# default
.LIBPATTERNS = lib%.so lib%.a
# makefile (from 'Makefile', line 146)
BIN_LIST_AUX = bowtie-build-debug bowtie-debug bowtie-inspect-debug
# default
LINK.C = $(LINK.cc)
# environment
PWD = /builddir/build/BUILD/bowtie-1.0.1
# environment
RPM_PACKAGE_VERSION = 1.0.1
# default
.LOADED := 
# default
LINK.S = $(CC) $(ASFLAGS) $(CPPFLAGS) $(LDFLAGS) $(TARGET_MACH)
# default
PREPROCESS.r = $(FC) $(FFLAGS) $(RFLAGS) $(TARGET_ARCH) -F
# environment
PKG_CONFIG_PATH = :/usr/lib64/pkgconfig:/usr/share/pkgconfig
# default
LINK.c = $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) $(TARGET_ARCH)
# default
LINK.s = $(CC) $(ASFLAGS) $(LDFLAGS) $(TARGET_MACH)
# environment
HOME = /builddir
# makefile (from 'Makefile', line 200)
ALL_FLAGS = $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)
# makefile (from 'Makefile', line 70)
POPCNT_CAPABILITY = 1
# automatic
-*-command-variables-*- := EXTRA_FLAGS=-O2\ -g\ -pipe\ -Wall\ -Werror=format-security\ -Wp,-D_FORTIFY_SOURCE=2\ -Wp,-D_GLIBCXX_ASSERTIONS\ -fexceptions\ -fstack-protector-strong\ -grecord-gcc-switches\ -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1\ 
# environment
LOGNAME = mockbuild
# default
LD = ld
# makefile (from 'Makefile', line 11)
HEADERS = $(wildcard *.h)
# makefile (from 'Makefile', line 13)
BOWTIE_SHARED_MEM = 1
# makefile (from 'Makefile', line 150)
GENERAL_LIST = $(wildcard scripts/*.sh) $(wildcard scripts/*.pl) $(wildcard indexes/e_coli*) $(wildcard genomes/NC_008253.fna) $(wildcard reads/e_coli_1000.*) $(wildcard reads/e_coli_1000_*) SeqAn-1.1 doc/manual.html doc/README doc/style.css reads/e_coli_10000snp.fa reads/e_coli_10000snp.fq $(PTHREAD_PKG) AUTHORS LICENSE NEWS MANUAL MANUAL.markdown TUTORIAL VERSION
# automatic
^D = $(patsubst %/,%,$(dir $^))
# environment
MAKELEVEL := 0
# environment
PYTHON_DISALLOW_AMBIGUOUS_VERSION = warn
# default
MAKE = $(MAKE_COMMAND)
# environment
SHLVL = 4
# default
AS = as
# makefile (from 'Makefile', line 12)
BOWTIE_MM = 1
# default
PREPROCESS.S = $(CC) -E $(CPPFLAGS)
# environment
MAKEOVERRIDES = ${-*-command-variables-*-}
# default
COMPILE.p = $(PC) $(PFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -c
# environment
XDG_SESSION_ID = c3
# environment
USER = mockbuild
# makefile (from 'Makefile', line 93)
SEARCH_CPPS_MAIN = $(SEARCH_CPPS) bowtie_main.cpp
# default
FC = f77
# makefile
.DEFAULT_GOAL := all
# makefile (from 'Makefile', line 80)
BUILD_LIBS = 
# automatic
%D = $(patsubst %/,%,$(dir $%))
# makefile (from 'Makefile', line 141)
FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
# makefile (from 'Makefile', line 81)
INSPECT_LIBS = 
# default
WEAVE = weave
# default
MAKE_COMMAND := make
# default
LINK.cpp = $(LINK.cc)
# default
F77 = $(FC)
# environment
OLDPWD = /builddir/build/BUILD
# default
.VARIABLES := 
# default
PC = pc
# automatic
*F = $(notdir $*)
# default
COMPILE.def = $(M2C) $(M2FLAGS) $(DEFFLAGS) $(TARGET_ARCH)
# default
LEX = lex
# default
RM = rm -f
# makefile
MAKEFLAGS = p -j4 --jobserver-auth=3,4 -- $(MAKEOVERRIDES)
# environment
MFLAGS = -p -j4 --jobserver-auth=3,4
# automatic
*D = $(patsubst %/,%,$(dir $*))
# makefile (from 'Makefile', line 202)
RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(ALL_FLAGS)\""
# default
LEX.l = $(LEX) $(LFLAGS) -t
# default
LEX.m = $(LEX) $(LFLAGS) -t
# makefile (from 'Makefile', line 5)
SEQAN_DIR = SeqAn-1.1
# automatic
+D = $(patsubst %/,%,$(dir $+))
# default
COMPILE.r = $(FC) $(FFLAGS) $(RFLAGS) $(TARGET_ARCH) -c
# automatic
+F = $(notdir $+)
# default
M2C = m2c
# makefile (from 'Makefile', line 47)
LINUX = 1
# environment
RPM_OS = linux
# makefile (from 'Makefile', line 59)
PTHREAD_PKG = 
# 'override' directive
.SHELLSTATUS := 0
# default
MAKEFILES := 
# default
COMPILE.cc = $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -c
# automatic
<F = $(notdir $<)
# makefile (from 'Makefile', line 137)
DEBUG_FLAGS = -O0 -g3 
# makefile (from 'Makefile', line 75)
PREFETCH_LOCALITY = 2
# makefile (from 'Makefile', line 9)
CXX = $(CPP)
# default
COFLAGS = 
# default
COMPILE.C = $(COMPILE.cc)
# makefile (from 'Makefile', line 78)
LIBS = $(PTHREAD_LIB)
# automatic
^F = $(notdir $^)
# environment
RPM_BUILD_ROOT = /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64
# default
COMPILE.S = $(CC) $(ASFLAGS) $(CPPFLAGS) $(TARGET_MACH) -c
# default
LINK.F = $(FC) $(FFLAGS) $(CPPFLAGS) $(LDFLAGS) $(TARGET_ARCH)
# default
SUFFIXES := .out .a .ln .o .c .cc .C .cpp .p .f .F .m .r .y .l .ym .yl .s .S .mod .sym .def .h .info .dvi .tex .texinfo .texi .txinfo .w .ch .web .sh .elc .el
# default
COMPILE.c = $(CC) $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -c
# makefile (from 'Makefile', line 7)
INC = $(SEQAN_INC) -I third_party
# default
COMPILE.s = $(AS) $(ASFLAGS) $(TARGET_MACH)
# default
.INCLUDE_DIRS = /usr/include /usr/local/include /usr/include
# environment
RPM_PACKAGE_RELEASE = 6.fc28
# makefile (from 'Makefile', line 15)
EXTRA_CFLAGS = 
# default
.RECIPEPREFIX := 
# default
MAKEINFO = makeinfo
# makefile (from 'Makefile', line 143)
BIN_LIST = bowtie-build bowtie bowtie-inspect
# default
OBJC = cc
# environment
RPM_PACKAGE_NAME = bowtie
# command line
EXTRA_FLAGS = -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 
# default
TEX = tex
# makefile (from 'Makefile', line 90)
SEARCH_CPPS = qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp
# environment
LANG = C
# environment
TERM = vt220
# default
F77FLAGS = $(FFLAGS)
# default
LINK.f = $(FC) $(FFLAGS) $(LDFLAGS) $(TARGET_ARCH)
# environment
RPM_ARCH = riscv64
# makefile (from 'Makefile', line 96)
BUILD_CPPS_MAIN = $(BUILD_CPPS) bowtie_build_main.cpp
# makefile (from 'Makefile', line 53)
MM_DEF = -DBOWTIE_MM
# variable set hash-table stats:
# Load=177/1024=17%, Rehash=0, Collisions=88/390=23%

# Pattern-specific Variable Values

# No pattern-specific variable values.

# Directories

# SCCS: could not be stat'd.
# third_party (device 65024, inode 786580): 3 files, no impossibilities.
# . (device 65024, inode 786450): 109 files, 65 impossibilities.
# scripts (device 65024, inode 786620): 37 files, no impossibilities.
# reads (device 65024, inode 786594): 11 files, no impossibilities.
# RCS: could not be stat'd.
# indexes (device 65024, inode 786703): 9 files, no impossibilities.

# 169 files, 65 impossibilities in 7 directories.

# Implicit Rules

%.out:

%.a:

%.ln:

%.o:

%: %.o
#  recipe to execute (built-in):
	$(LINK.o) $^ $(LOADLIBES) $(LDLIBS) -o $@

%.c:

%: %.c
#  recipe to execute (built-in):
	$(LINK.c) $^ $(LOADLIBES) $(LDLIBS) -o $@

%.ln: %.c
#  recipe to execute (built-in):
	$(LINT.c) -C$* $<

%.o: %.c
#  recipe to execute (built-in):
	$(COMPILE.c) $(OUTPUT_OPTION) $<

%.cc:

%: %.cc
#  recipe to execute (built-in):
	$(LINK.cc) $^ $(LOADLIBES) $(LDLIBS) -o $@

%.o: %.cc
#  recipe to execute (built-in):
	$(COMPILE.cc) $(OUTPUT_OPTION) $<

%.C:

%: %.C
#  recipe to execute (built-in):
	$(LINK.C) $^ $(LOADLIBES) $(LDLIBS) -o $@

%.o: %.C
#  recipe to execute (built-in):
	$(COMPILE.C) $(OUTPUT_OPTION) $<

%.cpp:

%: %.cpp
#  recipe to execute (built-in):
	$(LINK.cpp) $^ $(LOADLIBES) $(LDLIBS) -o $@

%.o: %.cpp
#  recipe to execute (built-in):
	$(COMPILE.cpp) $(OUTPUT_OPTION) $<

%.p:

%: %.p
#  recipe to execute (built-in):
	$(LINK.p) $^ $(LOADLIBES) $(LDLIBS) -o $@

%.o: %.p
#  recipe to execute (built-in):
	$(COMPILE.p) $(OUTPUT_OPTION) $<

%.f:

%: %.f
#  recipe to execute (built-in):
	$(LINK.f) $^ $(LOADLIBES) $(LDLIBS) -o $@

%.o: %.f
#  recipe to execute (built-in):
	$(COMPILE.f) $(OUTPUT_OPTION) $<

%.F:

%: %.F
#  recipe to execute (built-in):
	$(LINK.F) $^ $(LOADLIBES) $(LDLIBS) -o $@

%.o: %.F
#  recipe to execute (built-in):
	$(COMPILE.F) $(OUTPUT_OPTION) $<

%.f: %.F
#  recipe to execute (built-in):
	$(PREPROCESS.F) $(OUTPUT_OPTION) $<

%.m:

%: %.m
#  recipe to execute (built-in):
	$(LINK.m) $^ $(LOADLIBES) $(LDLIBS) -o $@

%.o: %.m
#  recipe to execute (built-in):
	$(COMPILE.m) $(OUTPUT_OPTION) $<

%.r:

%: %.r
#  recipe to execute (built-in):
	$(LINK.r) $^ $(LOADLIBES) $(LDLIBS) -o $@

%.o: %.r
#  recipe to execute (built-in):
	$(COMPILE.r) $(OUTPUT_OPTION) $<

%.f: %.r
#  recipe to execute (built-in):
	$(PREPROCESS.r) $(OUTPUT_OPTION) $<

%.y:

%.ln: %.y
#  recipe to execute (built-in):
	$(YACC.y) $< 
	 $(LINT.c) -C$* y.tab.c 
	 $(RM) y.tab.c

%.c: %.y
#  recipe to execute (built-in):
	$(YACC.y) $< 
	 mv -f y.tab.c $@

%.l:

%.ln: %.l
#  recipe to execute (built-in):
	@$(RM) $*.c
	 $(LEX.l) $< > $*.c
	$(LINT.c) -i $*.c -o $@
	 $(RM) $*.c

%.c: %.l
#  recipe to execute (built-in):
	@$(RM) $@ 
	 $(LEX.l) $< > $@

%.r: %.l
#  recipe to execute (built-in):
	$(LEX.l) $< > $@ 
	 mv -f lex.yy.r $@

%.ym:

%.m: %.ym
#  recipe to execute (built-in):
	$(YACC.m) $< 
	 mv -f y.tab.c $@

%.yl:

%.s:

%: %.s
#  recipe to execute (built-in):
	$(LINK.s) $^ $(LOADLIBES) $(LDLIBS) -o $@

%.o: %.s
#  recipe to execute (built-in):
	$(COMPILE.s) -o $@ $<

%.S:

%: %.S
#  recipe to execute (built-in):
	$(LINK.S) $^ $(LOADLIBES) $(LDLIBS) -o $@

%.o: %.S
#  recipe to execute (built-in):
	$(COMPILE.S) -o $@ $<

%.s: %.S
#  recipe to execute (built-in):
	$(PREPROCESS.S) $< > $@

%.mod:

%: %.mod
#  recipe to execute (built-in):
	$(COMPILE.mod) -o $@ -e $@ $^

%.o: %.mod
#  recipe to execute (built-in):
	$(COMPILE.mod) -o $@ $<

%.sym:

%.def:

%.sym: %.def
#  recipe to execute (built-in):
	$(COMPILE.def) -o $@ $<

%.h:

%.info:

%.dvi:

%.tex:

%.dvi: %.tex
#  recipe to execute (built-in):
	$(TEX) $<

%.texinfo:

%.info: %.texinfo
#  recipe to execute (built-in):
	$(MAKEINFO) $(MAKEINFO_FLAGS) $< -o $@

%.dvi: %.texinfo
#  recipe to execute (built-in):
	$(TEXI2DVI) $(TEXI2DVI_FLAGS) $<

%.texi:

%.info: %.texi
#  recipe to execute (built-in):
	$(MAKEINFO) $(MAKEINFO_FLAGS) $< -o $@

%.dvi: %.texi
#  recipe to execute (built-in):
	$(TEXI2DVI) $(TEXI2DVI_FLAGS) $<

%.txinfo:

%.info: %.txinfo
#  recipe to execute (built-in):
	$(MAKEINFO) $(MAKEINFO_FLAGS) $< -o $@

%.dvi: %.txinfo
#  recipe to execute (built-in):
	$(TEXI2DVI) $(TEXI2DVI_FLAGS) $<

%.w:

%.c: %.w
#  recipe to execute (built-in):
	$(CTANGLE) $< - $@

%.tex: %.w
#  recipe to execute (built-in):
	$(CWEAVE) $< - $@

%.ch:

%.web:

%.p: %.web
#  recipe to execute (built-in):
	$(TANGLE) $<

%.tex: %.web
#  recipe to execute (built-in):
	$(WEAVE) $<

%.sh:

%: %.sh
#  recipe to execute (built-in):
	cat $< >$@ 
	 chmod a+x $@

%.elc:

%.el:

(%): %
#  recipe to execute (built-in):
	$(AR) $(ARFLAGS) $@ $<

%.out: %
#  recipe to execute (built-in):
	@rm -f $@ 
	 cp $< $@

%.c: %.w %.ch
#  recipe to execute (built-in):
	$(CTANGLE) $^ $@

%.tex: %.w %.ch
#  recipe to execute (built-in):
	$(CWEAVE) $^ $@

%:: %,v
#  recipe to execute (built-in):
	$(CHECKOUT,v)

%:: RCS/%,v
#  recipe to execute (built-in):
	$(CHECKOUT,v)

%:: RCS/%
#  recipe to execute (built-in):
	$(CHECKOUT,v)

%:: s.%
#  recipe to execute (built-in):
	$(GET) $(GFLAGS) $(SCCS_OUTPUT_OPTION) $<

%:: SCCS/s.%
#  recipe to execute (built-in):
	$(GET) $(GFLAGS) $(SCCS_OUTPUT_OPTION) $<

# 92 implicit rules, 5 (5.4%) terminal.

# Files

# Not a target:
MANUAL.markdown:
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

# Not a target:
alphabet.cpp:
#  Implicit rule search has been done.
#  Last modified 2013-06-05 17:36:42
#  File has been updated.
#  Successfully updated.

# Not a target:
ebwt.h:
#  Implicit rule search has been done.
#  Last modified 2014-01-14 20:53:41
#  File has been updated.
#  Successfully updated.

bowtie-build_prof: ebwt_build.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp formats.h hit_set.h filebuf.h bitset.h hit.h log.h assert_helpers.h range_chaser.h range_cache.h timer.h ebwt.h mm.h blockwise_sa.h endian_swap.h ref_aligner.h pat.h ebwt_search_backtrack.h annot.h color_dec.h bitpack.h tokenize.h zbox.h sam.h random_source.h reference.h multikey_qsort.h range_source.h auto_array.h word_io.h edit.h fast_mutex.h aligner.h alphabet.h qual.h tinythread.h binary_sa_search.h threading.h range.h ref_read.h aligner_23mm.h row_chaser.h color.h refmap.h sequence_io.h aligner_1mm.h aligner_0mm.h shmem.h str_util.h processor_support.h pool.h ebwt_search_util.h search_globals.h diff_sample.h aligner_seed_mm.h aligner_metrics.h
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.
#  recipe to execute (from 'Makefile', line 217):
	$(CXX) $(RELEASE_FLAGS) -pg -p -g3 $(RELEASE_DEFS) $(ALL_FLAGS) \
		$(DEFS) $(NOASSERT_FLAGS) -Wall \
		$(INC) \
		-o $@ $< \
		$(OTHER_CPPS) $(BUILD_CPPS_MAIN) \
		$(LIBS) $(BUILD_LIBS)

# Not a target:
scripts/make_hg18.sh:
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

# Not a target:
scripts/random_bowtie_tests_p.sh:
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

# Not a target:
.web.p:
#  Builtin rule
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.
#  recipe to execute (built-in):
	$(TANGLE) $<

# Not a target:
search_exact.c:
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

bowtie-debug: ebwt_search.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp formats.h hit_set.h filebuf.h bitset.h hit.h log.h assert_helpers.h range_chaser.h range_cache.h timer.h ebwt.h mm.h blockwise_sa.h endian_swap.h ref_aligner.h pat.h ebwt_search_backtrack.h annot.h color_dec.h bitpack.h tokenize.h zbox.h sam.h random_source.h reference.h multikey_qsort.h range_source.h auto_array.h word_io.h edit.h fast_mutex.h aligner.h alphabet.h qual.h tinythread.h binary_sa_search.h threading.h range.h ref_read.h aligner_23mm.h row_chaser.h color.h refmap.h sequence_io.h aligner_1mm.h aligner_0mm.h shmem.h str_util.h processor_support.h pool.h ebwt_search_util.h search_globals.h diff_sample.h aligner_seed_mm.h aligner_metrics.h search_seeded_phase2.c search_23mm_phase2.c search_23mm_phase3.c search_seeded_phase3.c search_1mm_phase1.c search_seeded_phase4.c search_23mm_phase1.c search_seeded_phase1.c search_1mm_phase2.c
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.
#  recipe to execute (from 'Makefile', line 254):
	$(CXX) $(DEBUG_FLAGS) \
		$(DEBUG_DEFS) $(ALL_FLAGS) \
		$(DEFS) -Wall \
		$(INC) \
		-o $@ $< \
		$(OTHER_CPPS) $(SEARCH_CPPS_MAIN) \
		$(LIBS) $(SEARCH_LIBS)

bowtie-build-debug: ebwt_build.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp formats.h hit_set.h filebuf.h bitset.h hit.h log.h assert_helpers.h range_chaser.h range_cache.h timer.h ebwt.h mm.h blockwise_sa.h endian_swap.h ref_aligner.h pat.h ebwt_search_backtrack.h annot.h color_dec.h bitpack.h tokenize.h zbox.h sam.h random_source.h reference.h multikey_qsort.h range_source.h auto_array.h word_io.h edit.h fast_mutex.h aligner.h alphabet.h qual.h tinythread.h binary_sa_search.h threading.h range.h ref_read.h aligner_23mm.h row_chaser.h color.h refmap.h sequence_io.h aligner_1mm.h aligner_0mm.h shmem.h str_util.h processor_support.h pool.h ebwt_search_util.h search_globals.h diff_sample.h aligner_seed_mm.h aligner_metrics.h
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.
#  recipe to execute (from 'Makefile', line 225):
	$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(ALL_FLAGS) \
		$(DEFS) -Wall \
		$(INC) \
		-o $@ $< \
		$(OTHER_CPPS) $(BUILD_CPPS_MAIN) \
		$(LIBS) $(BUILD_LIBS)

# Not a target:
threading.h:
#  Implicit rule search has been done.
#  Last modified 2013-06-05 17:36:43
#  File has been updated.
#  Successfully updated.

# Not a target:
color.h:
#  Implicit rule search has been done.
#  Last modified 2013-06-05 17:36:42
#  File has been updated.
#  Successfully updated.

# Not a target:
scripts/gen_dnamasks2colormask.pl:
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

# Not a target:
indexes/e_coli.rev.1.ebwt:
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

# Not a target:
.l.r:
#  Builtin rule
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.
#  recipe to execute (built-in):
	$(LEX.l) $< > $@ 
	 mv -f lex.yy.r $@

# Not a target:
scripts/make_mm8.sh:
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

# Not a target:
search_23mm_phase2.c:
#  Implicit rule search has been done.
#  Last modified 2013-06-05 17:36:43
#  File has been updated.
#  Successfully updated.

# Not a target:
.dvi:
#  Builtin rule
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

# Not a target:
VERSION:
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

bowtie-inspect-debug: bowtie_inspect.cpp formats.h hit_set.h filebuf.h bitset.h hit.h log.h assert_helpers.h range_chaser.h range_cache.h timer.h ebwt.h mm.h blockwise_sa.h endian_swap.h ref_aligner.h pat.h ebwt_search_backtrack.h annot.h color_dec.h bitpack.h tokenize.h zbox.h sam.h random_source.h reference.h multikey_qsort.h range_source.h auto_array.h word_io.h edit.h fast_mutex.h aligner.h alphabet.h qual.h tinythread.h binary_sa_search.h threading.h range.h ref_read.h aligner_23mm.h row_chaser.h color.h refmap.h sequence_io.h aligner_1mm.h aligner_0mm.h shmem.h str_util.h processor_support.h pool.h ebwt_search_util.h search_globals.h diff_sample.h aligner_seed_mm.h aligner_metrics.h ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.
#  recipe to execute (from 'Makefile', line 276):
	$(CXX) $(DEBUG_FLAGS) \
		$(DEBUG_DEFS) $(ALL_FLAGS) \
		$(DEFS) -Wall \
		$(INC) -I . \
		-o $@ $< \
		$(OTHER_CPPS) \
		$(LIBS)

# Not a target:
indexes/e_coli.2.ebwt:
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

# Not a target:
search_seeded_phase2.c:
#  Implicit rule search has been done.
#  Last modified 2013-06-05 17:36:43
#  File has been updated.
#  Successfully updated.

# Not a target:
.ym:
#  Builtin rule
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

# Not a target:
scripts/make_mm9.sh:
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

# Not a target:
scripts/convert_quals.pl:
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

# Not a target:
.f.o:
#  Builtin rule
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.
#  recipe to execute (built-in):
	$(COMPILE.f) $(OUTPUT_OPTION) $<

# Not a target:
search_seeded_phase3.c:
#  Implicit rule search has been done.
#  Last modified 2013-06-05 17:36:43
#  File has been updated.
#  Successfully updated.

# Not a target:
annot.cpp:
#  Implicit rule search has been done.
#  Last modified 2013-06-05 17:36:42
#  File has been updated.
#  Successfully updated.

# Not a target:
.l:
#  Builtin rule
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

# Not a target:
.m:
#  Builtin rule
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.
#  recipe to execute (built-in):
	$(LINK.m) $^ $(LOADLIBES) $(LDLIBS) -o $@

# Not a target:
.ln:
#  Builtin rule
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

# Not a target:
.o:
#  Builtin rule
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.
#  recipe to execute (built-in):
	$(LINK.o) $^ $(LOADLIBES) $(LDLIBS) -o $@

bowtie: ebwt_search.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp formats.h hit_set.h filebuf.h bitset.h hit.h log.h assert_helpers.h range_chaser.h range_cache.h timer.h ebwt.h mm.h blockwise_sa.h endian_swap.h ref_aligner.h pat.h ebwt_search_backtrack.h annot.h color_dec.h bitpack.h tokenize.h zbox.h sam.h random_source.h reference.h multikey_qsort.h range_source.h auto_array.h word_io.h edit.h fast_mutex.h aligner.h alphabet.h qual.h tinythread.h binary_sa_search.h threading.h range.h ref_read.h aligner_23mm.h row_chaser.h color.h refmap.h sequence_io.h aligner_1mm.h aligner_0mm.h shmem.h str_util.h processor_support.h pool.h ebwt_search_util.h search_globals.h diff_sample.h aligner_seed_mm.h aligner_metrics.h search_seeded_phase2.c search_23mm_phase2.c search_23mm_phase3.c search_seeded_phase3.c search_1mm_phase1.c search_seeded_phase4.c search_23mm_phase1.c search_seeded_phase1.c search_1mm_phase2.c
#  Implicit rule search has not been done.
#  Implicit/static pattern stem: ''
#  Last modified 2018-02-23 20:29:56.872
#  File has been updated.
#  Successfully updated.
# automatic
# @ := bowtie
# automatic
# % := 
# automatic
# * := 
# automatic
# + := ebwt_search.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp formats.h hit_set.h filebuf.h bitset.h hit.h log.h assert_helpers.h range_chaser.h range_cache.h timer.h ebwt.h mm.h blockwise_sa.h endian_swap.h ref_aligner.h pat.h ebwt_search_backtrack.h annot.h color_dec.h bitpack.h tokenize.h zbox.h sam.h random_source.h reference.h multikey_qsort.h range_source.h auto_array.h word_io.h edit.h fast_mutex.h aligner.h alphabet.h qual.h tinythread.h binary_sa_search.h threading.h range.h ref_read.h aligner_23mm.h row_chaser.h color.h refmap.h sequence_io.h aligner_1mm.h aligner_0mm.h shmem.h str_util.h processor_support.h pool.h ebwt_search_util.h search_globals.h diff_sample.h aligner_seed_mm.h aligner_metrics.h search_seeded_phase2.c search_23mm_phase2.c search_23mm_phase3.c search_seeded_phase3.c search_1mm_phase1.c search_seeded_phase4.c search_23mm_phase1.c search_seeded_phase1.c search_1mm_phase2.c
# automatic
# | := 
# automatic
# < := ebwt_search.cpp
# automatic
# ^ := ebwt_search.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp formats.h hit_set.h filebuf.h bitset.h hit.h log.h assert_helpers.h range_chaser.h range_cache.h timer.h ebwt.h mm.h blockwise_sa.h endian_swap.h ref_aligner.h pat.h ebwt_search_backtrack.h annot.h color_dec.h bitpack.h tokenize.h zbox.h sam.h random_source.h reference.h multikey_qsort.h range_source.h auto_array.h word_io.h edit.h fast_mutex.h aligner.h alphabet.h qual.h tinythread.h binary_sa_search.h threading.h range.h ref_read.h aligner_23mm.h row_chaser.h color.h refmap.h sequence_io.h aligner_1mm.h aligner_0mm.h shmem.h str_util.h processor_support.h pool.h ebwt_search_util.h search_globals.h diff_sample.h aligner_seed_mm.h aligner_metrics.h search_seeded_phase2.c search_23mm_phase2.c search_23mm_phase3.c search_seeded_phase3.c search_1mm_phase1.c search_seeded_phase4.c search_23mm_phase1.c search_seeded_phase1.c search_1mm_phase2.c
# automatic
# ? := ebwt_search.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp formats.h hit_set.h filebuf.h bitset.h hit.h log.h assert_helpers.h range_chaser.h range_cache.h timer.h ebwt.h mm.h blockwise_sa.h endian_swap.h ref_aligner.h pat.h ebwt_search_backtrack.h annot.h color_dec.h bitpack.h tokenize.h zbox.h sam.h random_source.h reference.h multikey_qsort.h range_source.h auto_array.h word_io.h edit.h fast_mutex.h aligner.h alphabet.h qual.h tinythread.h binary_sa_search.h threading.h range.h ref_read.h aligner_23mm.h row_chaser.h color.h refmap.h sequence_io.h aligner_1mm.h aligner_0mm.h shmem.h str_util.h processor_support.h pool.h ebwt_search_util.h search_globals.h diff_sample.h aligner_seed_mm.h aligner_metrics.h search_seeded_phase2.c search_23mm_phase2.c search_23mm_phase3.c search_seeded_phase3.c search_1mm_phase1.c search_seeded_phase4.c search_23mm_phase1.c search_seeded_phase1.c search_1mm_phase2.c
# variable set hash-table stats:
# Load=8/32=25%, Rehash=0, Collisions=8/51=16%
#  recipe to execute (from 'Makefile', line 237):
	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(ALL_FLAGS) \
		$(DEFS) $(NOASSERT_FLAGS) -Wall \
		$(INC) \
		-o $@ $< \
		$(OTHER_CPPS) $(SEARCH_CPPS_MAIN) \
		$(LIBS) $(SEARCH_LIBS)

# Not a target:
bowtie_build_main.cpp:
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

# Not a target:
.y:
#  Builtin rule
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

# Not a target:
.def.sym:
#  Builtin rule
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.
#  recipe to execute (built-in):
	$(COMPILE.def) -o $@ $<

# Not a target:
ref_read.h:
#  Implicit rule search has been done.
#  Last modified 2013-06-05 17:36:43
#  File has been updated.
#  Successfully updated.

.PHONY: doc clean
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

# Not a target:
indexes/e_coli.rev.2.ebwt:
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

# Not a target:
qual.cpp:
#  Implicit rule search has been done.
#  Last modified 2013-06-05 17:36:43
#  File has been updated.
#  Successfully updated.

# Not a target:
reads/e_coli_1000_2.fq:
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

# Not a target:
.p.o:
#  Builtin rule
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.
#  recipe to execute (built-in):
	$(COMPILE.p) $(OUTPUT_OPTION) $<

# Not a target:
.p:
#  Builtin rule
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.
#  recipe to execute (built-in):
	$(LINK.p) $^ $(LOADLIBES) $(LDLIBS) -o $@

# Not a target:
annot.h:
#  Implicit rule search has been done.
#  Last modified 2013-06-05 17:36:42
#  File has been updated.
#  Successfully updated.

# Not a target:
hit_set.h:
#  Implicit rule search has been done.
#  Last modified 2013-06-05 17:36:43
#  File has been updated.
#  Successfully updated.

# Not a target:
.txinfo.dvi:
#  Builtin rule
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.
#  recipe to execute (built-in):
	$(TEXI2DVI) $(TEXI2DVI_FLAGS) $<

# Not a target:
tinythread.h:
#  Implicit rule search has been done.
#  Last modified 2013-06-05 17:36:43
#  File has been updated.
#  Successfully updated.

# Not a target:
ebwt.cpp:
#  Implicit rule search has been done.
#  Last modified 2013-06-05 17:36:42
#  File has been updated.
#  Successfully updated.

# Not a target:
scripts/make_c_elegans.sh:
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

# Not a target:
.a:
#  Builtin rule
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	 $(RM) $*.c

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.SUFFIXES: .out .a .ln .o .c .cc .C .cpp .p .f .F .m .r .y .l .ym .yl .s .S .mod .sym .def .h .info .dvi .tex .texinfo .texi .txinfo .w .ch .web .sh .elc .el
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hit.cpp:
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allall: bowtie-build bowtie bowtie-inspect bowtie-build-debug bowtie-debug bowtie-inspect-debug
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	$(YACC.y) $< 
	 $(LINT.c) -C$* y.tab.c 
	 $(RM) y.tab.c

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all: bowtie-build bowtie bowtie-inspect
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# variable set hash-table stats:
# Load=0/32=0%, Rehash=0, Collisions=0/119=0%

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bowtie-inspect: bowtie_inspect.cpp formats.h hit_set.h filebuf.h bitset.h hit.h log.h assert_helpers.h range_chaser.h range_cache.h timer.h ebwt.h mm.h blockwise_sa.h endian_swap.h ref_aligner.h pat.h ebwt_search_backtrack.h annot.h color_dec.h bitpack.h tokenize.h zbox.h sam.h random_source.h reference.h multikey_qsort.h range_source.h auto_array.h word_io.h edit.h fast_mutex.h aligner.h alphabet.h qual.h tinythread.h binary_sa_search.h threading.h range.h ref_read.h aligner_23mm.h row_chaser.h color.h refmap.h sequence_io.h aligner_1mm.h aligner_0mm.h shmem.h str_util.h processor_support.h pool.h ebwt_search_util.h search_globals.h diff_sample.h aligner_seed_mm.h aligner_metrics.h ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp
#  Implicit rule search has not been done.
#  Implicit/static pattern stem: ''
#  Last modified 2018-02-23 20:08:40.644
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# automatic
# @ := bowtie-inspect
# automatic
# % := 
# automatic
# * := 
# automatic
# + := bowtie_inspect.cpp formats.h hit_set.h filebuf.h bitset.h hit.h log.h assert_helpers.h range_chaser.h range_cache.h timer.h ebwt.h mm.h blockwise_sa.h endian_swap.h ref_aligner.h pat.h ebwt_search_backtrack.h annot.h color_dec.h bitpack.h tokenize.h zbox.h sam.h random_source.h reference.h multikey_qsort.h range_source.h auto_array.h word_io.h edit.h fast_mutex.h aligner.h alphabet.h qual.h tinythread.h binary_sa_search.h threading.h range.h ref_read.h aligner_23mm.h row_chaser.h color.h refmap.h sequence_io.h aligner_1mm.h aligner_0mm.h shmem.h str_util.h processor_support.h pool.h ebwt_search_util.h search_globals.h diff_sample.h aligner_seed_mm.h aligner_metrics.h ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp
# automatic
# | := 
# automatic
# < := bowtie_inspect.cpp
# automatic
# ^ := bowtie_inspect.cpp formats.h hit_set.h filebuf.h bitset.h hit.h log.h assert_helpers.h range_chaser.h range_cache.h timer.h ebwt.h mm.h blockwise_sa.h endian_swap.h ref_aligner.h pat.h ebwt_search_backtrack.h annot.h color_dec.h bitpack.h tokenize.h zbox.h sam.h random_source.h reference.h multikey_qsort.h range_source.h auto_array.h word_io.h edit.h fast_mutex.h aligner.h alphabet.h qual.h tinythread.h binary_sa_search.h threading.h range.h ref_read.h aligner_23mm.h row_chaser.h color.h refmap.h sequence_io.h aligner_1mm.h aligner_0mm.h shmem.h str_util.h processor_support.h pool.h ebwt_search_util.h search_globals.h diff_sample.h aligner_seed_mm.h aligner_metrics.h ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp
# automatic
# ? := bowtie_inspect.cpp formats.h hit_set.h filebuf.h bitset.h hit.h log.h assert_helpers.h range_chaser.h range_cache.h timer.h ebwt.h mm.h blockwise_sa.h endian_swap.h ref_aligner.h pat.h ebwt_search_backtrack.h annot.h color_dec.h bitpack.h tokenize.h zbox.h sam.h random_source.h reference.h multikey_qsort.h range_source.h auto_array.h word_io.h edit.h fast_mutex.h aligner.h alphabet.h qual.h tinythread.h binary_sa_search.h threading.h range.h ref_read.h aligner_23mm.h row_chaser.h color.h refmap.h sequence_io.h aligner_1mm.h aligner_0mm.h shmem.h str_util.h processor_support.h pool.h ebwt_search_util.h search_globals.h diff_sample.h aligner_seed_mm.h aligner_metrics.h ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp
# variable set hash-table stats:
# Load=8/32=25%, Rehash=0, Collisions=6/47=13%
#  recipe to execute (from 'Makefile', line 267):
	$(CXX) $(RELEASE_FLAGS) \
		$(RELEASE_DEFS) $(ALL_FLAGS) \
		$(DEFS) -Wall \
		$(INC) -I . \
		-o $@ $< \
		$(OTHER_CPPS) \
		$(LIBS)

# Not a target:
.S:
#  Builtin rule
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.
#  recipe to execute (built-in):
	$(LINK.S) $^ $(LOADLIBES) $(LDLIBS) -o $@

# Not a target:
range_source.h:
#  Implicit rule search has been done.
#  Last modified 2013-06-05 17:36:43
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# Not a target:
.texinfo.info:
#  Builtin rule
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#  Modification time never checked.
#  File has not been updated.
#  recipe to execute (built-in):
	$(MAKEINFO) $(MAKEINFO_FLAGS) $< -o $@

# Not a target:
ebwt_search_util.h:
#  Implicit rule search has been done.
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# Not a target:
.c:
#  Builtin rule
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#  Modification time never checked.
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#  recipe to execute (built-in):
	$(LINK.c) $^ $(LOADLIBES) $(LDLIBS) -o $@

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.w.tex:
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#  Modification time never checked.
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#  recipe to execute (built-in):
	$(CWEAVE) $< - $@

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fast_mutex.h:
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#  Last modified 2013-06-05 17:36:42
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# Not a target:
.c.ln:
#  Builtin rule
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#  Modification time never checked.
#  File has not been updated.
#  recipe to execute (built-in):
	$(LINT.c) -C$* $<

# Not a target:
.s.o:
#  Builtin rule
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#  Modification time never checked.
#  File has not been updated.
#  recipe to execute (built-in):
	$(COMPILE.s) -o $@ $<

# Not a target:
.s:
#  Builtin rule
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.
#  recipe to execute (built-in):
	$(LINK.s) $^ $(LOADLIBES) $(LDLIBS) -o $@

# Not a target:
doc/README:
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#  Modification time never checked.
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# Not a target:
log.h:
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#  Last modified 2014-03-19 15:07:45
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#  Successfully updated.

# Not a target:
TUTORIAL:
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#  Modification time never checked.
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# Not a target:
range_cache.h:
#  Implicit rule search has been done.
#  Last modified 2013-06-05 17:36:43
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#  Successfully updated.

# Not a target:
search_1mm_phase2.c:
#  Implicit rule search has been done.
#  Last modified 2013-06-05 17:36:43
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#  Successfully updated.

# Not a target:
color_dec.cpp:
#  Implicit rule search has been done.
#  Last modified 2013-06-05 17:36:42
#  File has been updated.
#  Successfully updated.

# Not a target:
scripts/make_e_coli.sh:
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.

# Not a target:
ebwt_search_util.cpp:
#  Implicit rule search has been done.
#  Last modified 2013-06-05 17:36:42
#  File has been updated.
#  Successfully updated.

bowtie-build: ebwt_build.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp formats.h hit_set.h filebuf.h bitset.h hit.h log.h assert_helpers.h range_chaser.h range_cache.h timer.h ebwt.h mm.h blockwise_sa.h endian_swap.h ref_aligner.h pat.h ebwt_search_backtrack.h annot.h color_dec.h bitpack.h tokenize.h zbox.h sam.h random_source.h reference.h multikey_qsort.h range_source.h auto_array.h word_io.h edit.h fast_mutex.h aligner.h alphabet.h qual.h tinythread.h binary_sa_search.h threading.h range.h ref_read.h aligner_23mm.h row_chaser.h color.h refmap.h sequence_io.h aligner_1mm.h aligner_0mm.h shmem.h str_util.h processor_support.h pool.h ebwt_search_util.h search_globals.h diff_sample.h aligner_seed_mm.h aligner_metrics.h
#  Implicit rule search has not been done.
#  Implicit/static pattern stem: ''
#  Last modified 2018-02-23 20:08:50.22
#  File has been updated.
#  Successfully updated.
# automatic
# @ := bowtie-build
# automatic
# % := 
# automatic
# * := 
# automatic
# + := ebwt_build.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp formats.h hit_set.h filebuf.h bitset.h hit.h log.h assert_helpers.h range_chaser.h range_cache.h timer.h ebwt.h mm.h blockwise_sa.h endian_swap.h ref_aligner.h pat.h ebwt_search_backtrack.h annot.h color_dec.h bitpack.h tokenize.h zbox.h sam.h random_source.h reference.h multikey_qsort.h range_source.h auto_array.h word_io.h edit.h fast_mutex.h aligner.h alphabet.h qual.h tinythread.h binary_sa_search.h threading.h range.h ref_read.h aligner_23mm.h row_chaser.h color.h refmap.h sequence_io.h aligner_1mm.h aligner_0mm.h shmem.h str_util.h processor_support.h pool.h ebwt_search_util.h search_globals.h diff_sample.h aligner_seed_mm.h aligner_metrics.h
# automatic
# | := 
# automatic
# < := ebwt_build.cpp
# automatic
# ^ := ebwt_build.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp formats.h hit_set.h filebuf.h bitset.h hit.h log.h assert_helpers.h range_chaser.h range_cache.h timer.h ebwt.h mm.h blockwise_sa.h endian_swap.h ref_aligner.h pat.h ebwt_search_backtrack.h annot.h color_dec.h bitpack.h tokenize.h zbox.h sam.h random_source.h reference.h multikey_qsort.h range_source.h auto_array.h word_io.h edit.h fast_mutex.h aligner.h alphabet.h qual.h tinythread.h binary_sa_search.h threading.h range.h ref_read.h aligner_23mm.h row_chaser.h color.h refmap.h sequence_io.h aligner_1mm.h aligner_0mm.h shmem.h str_util.h processor_support.h pool.h ebwt_search_util.h search_globals.h diff_sample.h aligner_seed_mm.h aligner_metrics.h
# automatic
# ? := ebwt_build.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp formats.h hit_set.h filebuf.h bitset.h hit.h log.h assert_helpers.h range_chaser.h range_cache.h timer.h ebwt.h mm.h blockwise_sa.h endian_swap.h ref_aligner.h pat.h ebwt_search_backtrack.h annot.h color_dec.h bitpack.h tokenize.h zbox.h sam.h random_source.h reference.h multikey_qsort.h range_source.h auto_array.h word_io.h edit.h fast_mutex.h aligner.h alphabet.h qual.h tinythread.h binary_sa_search.h threading.h range.h ref_read.h aligner_23mm.h row_chaser.h color.h refmap.h sequence_io.h aligner_1mm.h aligner_0mm.h shmem.h str_util.h processor_support.h pool.h ebwt_search_util.h search_globals.h diff_sample.h aligner_seed_mm.h aligner_metrics.h
# variable set hash-table stats:
# Load=8/32=25%, Rehash=0, Collisions=7/51=14%
#  recipe to execute (from 'Makefile', line 209):
	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(ALL_FLAGS)  \
		$(DEFS) $(NOASSERT_FLAGS) -Wall \
		$(INC) \
		-o $@ $< \
		$(OTHER_CPPS) $(BUILD_CPPS_MAIN) \
		$(LIBS) $(BUILD_LIBS)

# Not a target:
.texinfo.dvi:
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#  recipe to execute (built-in):
	$(TEXI2DVI) $(TEXI2DVI_FLAGS) $<

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# Not a target:
log.cpp:
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#  Last modified 2013-06-05 17:36:43
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# Not a target:
.lm.m:
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#  recipe to execute (built-in):
	@$(RM) $@ 
	 $(LEX.m) $< > $@

# Not a target:
aligner.h:
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# Not a target:
scripts/make_b_taurus_UMD3.sh:
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.y.c:
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#  recipe to execute (built-in):
	$(YACC.y) $< 
	 mv -f y.tab.c $@

bowtie-bin.zip: scripts/make_b_taurus_UMD3.sh scripts/random_bowtie_tests_p.sh scripts/make_e_coli.sh scripts/make_h_sapiens_ncbi36.sh scripts/make_hg19.sh scripts/random_bowtie_tests.sh scripts/make_rn4.sh scripts/make_galGal3.sh scripts/make_hg18.sh scripts/make_m_musculus_ncbi37.sh scripts/make_a_thaliana_tair.sh scripts/make_mm9.sh scripts/make_s_cerevisiae.sh scripts/make_c_elegans.sh scripts/make_h_sapiens_ncbi37.sh scripts/build_test.sh scripts/make_d_melanogaster.sh scripts/make_mm8.sh scripts/make_canFam2.sh scripts/gen_dnamasks2colormask.pl scripts/pe_verify.pl scripts/gen_occ_lookup.pl scripts/bs_mapability.pl scripts/fastq_to_tabbed.pl scripts/random_bowtie_tests.pl scripts/reconcile_alignments.pl scripts/mapability.pl scripts/colorize_fasta.pl scripts/colorize_fastq.pl scripts/convert_quals.pl scripts/reconcile_alignments_pe.pl scripts/infer_fraglen.pl scripts/gen_solqual_lookup.pl scripts/gen_2b_occ_lookup.pl scripts/best_verify.pl indexes/e_coli.README indexes/e_coli.2.ebwt indexes/e_coli.rev.1.ebwt indexes/e_coli.rev.2.ebwt indexes/e_coli.4.ebwt indexes/e_coli.1.ebwt indexes/e_coli.3.ebwt genomes/NC_008253.fna reads/e_coli_1000.fa reads/e_coli_1000.raw reads/e_coli_1000.fq reads/e_coli_1000_2.fa reads/e_coli_1000_1.fq reads/e_coli_1000_1.fa reads/e_coli_1000_2.fq SeqAn-1.1 doc/manual.html doc/README doc/style.css reads/e_coli_10000snp.fa reads/e_coli_10000snp.fq AUTHORS LICENSE NEWS MANUAL MANUAL.markdown TUTORIAL VERSION bowtie-build bowtie bowtie-inspect bowtie-build-debug bowtie-debug bowtie-inspect-debug
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.
#  recipe to execute (from 'Makefile', line 296):
	chmod a+x scripts/*.sh scripts/*.pl
	rm -rf .bin.tmp
	mkdir .bin.tmp
	mkdir .bin.tmp/bowtie-$(VERSION)
	if [ -f bowtie.exe ] ; then \
		zip tmp.zip $(BIN_PKG_LIST) $(addsuffix .exe,$(BIN_LIST) $(BIN_LIST_AUX)) ; \
	else \
		zip tmp.zip $(BIN_PKG_LIST) $(BIN_LIST) $(BIN_LIST_AUX) ; \
	fi
	mv tmp.zip .bin.tmp/bowtie-$(VERSION)
	cd .bin.tmp/bowtie-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
	cd .bin.tmp ; zip -r $@ bowtie-$(VERSION)
	cp .bin.tmp/$@ .
	rm -rf .bin.tmp

# Not a target:
.web.tex:
#  Builtin rule
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#  recipe to execute (built-in):
	$(WEAVE) $<

# Not a target:
.texinfo:
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bowtie_prof: ebwt_search.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp formats.h hit_set.h filebuf.h bitset.h hit.h log.h assert_helpers.h range_chaser.h range_cache.h timer.h ebwt.h mm.h blockwise_sa.h endian_swap.h ref_aligner.h pat.h ebwt_search_backtrack.h annot.h color_dec.h bitpack.h tokenize.h zbox.h sam.h random_source.h reference.h multikey_qsort.h range_source.h auto_array.h word_io.h edit.h fast_mutex.h aligner.h alphabet.h qual.h tinythread.h binary_sa_search.h threading.h range.h ref_read.h aligner_23mm.h row_chaser.h color.h refmap.h sequence_io.h aligner_1mm.h aligner_0mm.h shmem.h str_util.h processor_support.h pool.h ebwt_search_util.h search_globals.h diff_sample.h aligner_seed_mm.h aligner_metrics.h search_seeded_phase2.c search_23mm_phase2.c search_23mm_phase3.c search_seeded_phase3.c search_1mm_phase1.c search_seeded_phase4.c search_23mm_phase1.c search_seeded_phase1.c search_1mm_phase2.c
#  Implicit rule search has not been done.
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#  File has not been updated.
#  recipe to execute (from 'Makefile', line 245):
	$(CXX) $(RELEASE_FLAGS) \
		$(RELEASE_DEFS) -pg -p -g3 $(ALL_FLAGS) \
		$(DEFS) $(NOASSERT_FLAGS) -Wall \
		$(INC) \
		-o $@ $< \
		$(OTHER_CPPS) $(SEARCH_CPPS_MAIN) \
		$(LIBS) $(SEARCH_LIBS)

# Not a target:
aligner_metrics.h:
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scripts/make_h_sapiens_ncbi36.sh:
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.h:
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scripts/best_verify.pl:
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pool.h:
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indexes/e_coli.4.ebwt:
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ref_aligner.h:
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# Not a target:
aligner_seed_mm.h:
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# Not a target:
shmem.h:
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str_util.h:
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aligner_0mm.h:
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#  recipe to execute (built-in):
	$(TEX) $<

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formats.h:
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#  recipe to execute (built-in):
	$(COMPILE.cpp) $(OUTPUT_OPTION) $<

# Not a target:
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#  Builtin rule
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#  recipe to execute (built-in):
	$(LINK.cpp) $^ $(LOADLIBES) $(LDLIBS) -o $@

clean:
#  Phony target (prerequisite of .PHONY).
#  Implicit rule search has not been done.
#  File does not exist.
#  File has not been updated.
#  recipe to execute (from 'Makefile', line 326):
	rm -f $(BIN_LIST) $(BIN_LIST_AUX) \
	bowtie_prof \
	$(addsuffix .exe,$(BIN_LIST) $(BIN_LIST_AUX) bowtie_prof) \
	bowtie-src.zip bowtie-bin.zip
	rm -f core.*

# Not a target:
.C.o:
#  Builtin rule
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#  recipe to execute (built-in):
	$(COMPILE.C) $(OUTPUT_OPTION) $<

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scripts/bs_mapability.pl:
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ref_aligner.cpp:
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.tex:
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binary_sa_search.h:
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blockwise_sa.h:
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# Not a target:
scripts/make_a_thaliana_tair.sh:
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#  recipe to execute (built-in):
	$(MAKEINFO) $(MAKEINFO_FLAGS) $< -o $@

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scripts/colorize_fastq.pl:
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MANUAL: MANUAL.markdown
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#  recipe to execute (from 'Makefile', line 322):
	perl doc/strip_markdown.pl < $^ > $@

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scripts/mapability.pl:
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aligner_1mm.h:
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filebuf.h:
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search_globals.h:
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tokenize.h:
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reads/e_coli_1000.fa:
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scripts/make_galGal3.sh:
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reads/e_coli_1000.fq:
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#  recipe to execute (built-in):
	cat $< >$@ 
	 chmod a+x $@

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range.h:
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ebwt_search_backtrack.h:
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ebwt_build.cpp:
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scripts/reconcile_alignments.pl:
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ebwt_search.cpp:
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edit.h:
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multikey_qsort.h:
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NEWS:
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sam.h:
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refmap.cpp:
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search_seeded_phase1.c:
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search_23mm_phase1.c:
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edit.cpp:
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processor_support.h:
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sam.cpp:
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genomes/NC_008253.fna:
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assert_helpers.h:
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bowtie-src.zip: formats.h hit_set.h filebuf.h bitset.h hit.h log.h assert_helpers.h range_chaser.h range_cache.h timer.h ebwt.h mm.h blockwise_sa.h endian_swap.h ref_aligner.h pat.h ebwt_search_backtrack.h annot.h color_dec.h bitpack.h tokenize.h zbox.h sam.h random_source.h reference.h multikey_qsort.h range_source.h auto_array.h word_io.h edit.h fast_mutex.h aligner.h alphabet.h qual.h tinythread.h binary_sa_search.h threading.h range.h ref_read.h aligner_23mm.h row_chaser.h color.h refmap.h sequence_io.h aligner_1mm.h aligner_0mm.h shmem.h str_util.h processor_support.h pool.h ebwt_search_util.h search_globals.h diff_sample.h aligner_seed_mm.h aligner_metrics.h search_exact.c search_seeded_phase2.c search_23mm_phase2.c search_23mm_phase3.c search_seeded_phase3.c search_1mm_phase1.c search_seeded_phase4.c search_23mm_phase1.c search_seeded_phase1.c search_1mm_phase2.c bowtie_inspect.cpp ccnt_lut.cpp bowtie_build_main.cpp refmap.cpp ebwt_search.cpp hit_set.cpp annot.cpp tinythread.cpp shmem.cpp ref_read.cpp ref_aligner.cpp hit.cpp random_test.cpp color_dec.cpp qual.cpp pat.cpp ebwt.cpp chaincat.cpp log.cpp bowtie_main.cpp sam.cpp ebwt_search_util.cpp edit.cpp ebwt_build.cpp color.cpp alphabet.cpp third_party/cpuid.h doc/strip_markdown.pl Makefile scripts/make_b_taurus_UMD3.sh scripts/random_bowtie_tests_p.sh scripts/make_e_coli.sh scripts/make_h_sapiens_ncbi36.sh scripts/make_hg19.sh scripts/random_bowtie_tests.sh scripts/make_rn4.sh scripts/make_galGal3.sh scripts/make_hg18.sh scripts/make_m_musculus_ncbi37.sh scripts/make_a_thaliana_tair.sh scripts/make_mm9.sh scripts/make_s_cerevisiae.sh scripts/make_c_elegans.sh scripts/make_h_sapiens_ncbi37.sh scripts/build_test.sh scripts/make_d_melanogaster.sh scripts/make_mm8.sh scripts/make_canFam2.sh scripts/gen_dnamasks2colormask.pl scripts/pe_verify.pl scripts/gen_occ_lookup.pl scripts/bs_mapability.pl scripts/fastq_to_tabbed.pl scripts/random_bowtie_tests.pl scripts/reconcile_alignments.pl scripts/mapability.pl scripts/colorize_fasta.pl scripts/colorize_fastq.pl scripts/convert_quals.pl scripts/reconcile_alignments_pe.pl scripts/infer_fraglen.pl scripts/gen_solqual_lookup.pl scripts/gen_2b_occ_lookup.pl scripts/best_verify.pl indexes/e_coli.README indexes/e_coli.2.ebwt indexes/e_coli.rev.1.ebwt indexes/e_coli.rev.2.ebwt indexes/e_coli.4.ebwt indexes/e_coli.1.ebwt indexes/e_coli.3.ebwt genomes/NC_008253.fna reads/e_coli_1000.fa reads/e_coli_1000.raw reads/e_coli_1000.fq reads/e_coli_1000_2.fa reads/e_coli_1000_1.fq reads/e_coli_1000_1.fa reads/e_coli_1000_2.fq SeqAn-1.1 doc/manual.html doc/README doc/style.css reads/e_coli_10000snp.fa reads/e_coli_10000snp.fq AUTHORS LICENSE NEWS MANUAL MANUAL.markdown TUTORIAL VERSION
#  Implicit rule search has not been done.
#  Modification time never checked.
#  File has not been updated.
#  recipe to execute (from 'Makefile', line 285):
	chmod a+x scripts/*.sh scripts/*.pl
	mkdir .src.tmp
	mkdir .src.tmp/bowtie-$(VERSION)
	zip -r tmp.zip $(SRC_PKG_LIST)
	mv tmp.zip .src.tmp/bowtie-$(VERSION)
	cd .src.tmp/bowtie-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
	cd .src.tmp ; zip -r $@ bowtie-$(VERSION)
	cp .src.tmp/$@ .
	rm -rf .src.tmp

# Not a target:
alphabet.h:
#  Implicit rule search has been done.
#  Last modified 2013-06-05 17:36:42
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# Not a target:
LICENSE:
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# Not a target:
.F:
#  Builtin rule
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#  File has not been updated.
#  recipe to execute (built-in):
	$(LINK.F) $^ $(LOADLIBES) $(LDLIBS) -o $@

# Not a target:
reads/e_coli_1000_1.fa:
#  Implicit rule search has not been done.
#  Modification time never checked.
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# Not a target:
color.cpp:
#  Implicit rule search has been done.
#  Last modified 2013-06-05 17:36:42
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# Not a target:
scripts/gen_2b_occ_lookup.pl:
#  Implicit rule search has not been done.
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# Not a target:
.web:
#  Builtin rule
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doc: doc/manual.html MANUAL
#  Phony target (prerequisite of .PHONY).
#  Implicit rule search has not been done.
#  File does not exist.
#  File has not been updated.

# Not a target:
reads/e_coli_1000_1.fq:
#  Implicit rule search has not been done.
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# Not a target:
.sym:
#  Builtin rule
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mm.h:
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#  Last modified 2013-06-05 17:36:43
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endian_swap.h:
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#  Last modified 2014-03-18 15:15:16
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.f:
#  Builtin rule
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#  Modification time never checked.
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#  recipe to execute (built-in):
	$(LINK.f) $^ $(LOADLIBES) $(LDLIBS) -o $@

doc/manual.html: MANUAL.markdown
#  Implicit rule search has not been done.
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#  recipe to execute (from 'Makefile', line 315):
	echo "<h1>Table of Contents</h1>" > .tmp.head
	pandoc -T "Bowtie Manual" -B .tmp.head \
	       --css style.css -o $@ \
	       --from markdown --to HTML \
	       --table-of-contents $^

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row_chaser.h:
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diff_sample.h:
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indexes/e_coli.1.ebwt:
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bowtie_inspect.cpp:
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# files hash-table stats:
# Load=244/1024=24%, Rehash=0, Collisions=1296/3252=40%
# VPATH Search Paths

# No 'vpath' search paths.

# No general ('VPATH' variable) search path.

# strcache buffers: 3 (2) / strings = 1179 / storage = 18976 B / avg = 16 B
# current buf: size = 8162 B / used = 2673 B / count = 106 / avg = 25 B
# other used: total = 16303 B / count = 1073 / avg = 15 B
# other free: total = 21 B / max = 11 B / min = 10 B / avg = 10 B

# strcache performance: lookups = 2299 / hit rate = 48%
# hash-table stats:
# Load=1179/8192=14%, Rehash=0, Collisions=378/2299=16%
# Finished Make data base on Fri Feb 23 20:29:57 2018

+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.WibUsm
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64
++ dirname /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64
+ cd bowtie-1.0.1
+ rm -rf /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64
+ mkdir -p /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64//usr/bin
+ mkdir -p /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64//usr/share/bowtie
+ install -m 0755 bowtie /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64//usr/bin
+ install -m 0755 bowtie-build /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64//usr/bin
+ install -m 0755 bowtie-inspect /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64//usr/bin
+ cp -a reads /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64//usr/share/bowtie/
+ cp -a indexes /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64//usr/share/bowtie/
+ cp -a genomes /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64//usr/share/bowtie/
+ cp -a scripts /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64//usr/share/bowtie/
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
/sbin/ldconfig: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf: No such file or directory
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/brp-strip /usr/bin/strip
+ /usr/lib/rpm/brp-strip-comment-note /usr/bin/strip /usr/bin/objdump
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1
+ /usr/lib/rpm/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
Processing files: bowtie-1.0.1-6.fc28.riscv64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.N6ZNrh
+ umask 022
+ cd /builddir/build/BUILD
+ cd bowtie-1.0.1
+ DOCDIR=/builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64/usr/share/doc/bowtie
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64/usr/share/doc/bowtie
+ cp -pr MANUAL /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64/usr/share/doc/bowtie
+ cp -pr NEWS /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64/usr/share/doc/bowtie
+ cp -pr VERSION /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64/usr/share/doc/bowtie
+ cp -pr AUTHORS /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64/usr/share/doc/bowtie
+ cp -pr TUTORIAL /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64/usr/share/doc/bowtie
+ cp -pr doc/manual.html doc/style.css /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64/usr/share/doc/bowtie
+ cp -pr SeqAn-1.1/GPL.txt SeqAn-1.1/LGPL.txt /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64/usr/share/doc/bowtie
+ exit 0
Provides: bowtie = 1.0.1-6.fc28 bowtie(riscv-64) = 1.0.1-6.fc28
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /bin/sh /usr/bin/perl ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.4)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.27)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) rtld(GNU_HASH)
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64
Wrote: /builddir/build/SRPMS/bowtie-1.0.1-6.fc28.src.rpm
Wrote: /builddir/build/RPMS/riscv64/bowtie-1.0.1-6.fc28.riscv64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.aIERMY
+ umask 022
+ cd /builddir/build/BUILD
+ cd bowtie-1.0.1
+ rm -rf /builddir/build/BUILDROOT/bowtie-1.0.1-6.fc28.riscv64
+ exit 0
+ touch /buildok
+ cleanup
+ set +e
+ sync
+ sleep 5
+ sync
+ poweroff
Terminated
++ cleanup
++ set +e
++ sync
Terminated
+++ cleanup
+++ set +e
+++ sync
+++ sleep 5
+++ sync
+++ poweroff