[Debian-med-packaging] Help needed to adapt latest Bowtie version to SeqAn 1.4

[Andreas Tille]

Hi,

I tried to build the latest Bowtie 1.1 but stumbled again about changes
which are most probably incompatible with the latest SeqAn library which
we are using instead of upstreams code copy of an old version.  Since I
never recieved any answer from Bowtie upstream I'm asking on Debian
Mentors and SeqAn upstream which might have an idea as well.  The build
error is


...
make[2]: Entering directory '/tmp/buildd/bowtie-1.1.0'
g++ -O3 -DCOMPILER_OPTIONS="\"-O3  -Wl,--hash-style=both -DPOPCNT_CAPABILITY -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -g -O2 -fstack-protector-strong -Wformat -Werro
<------>-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
<------>-I /usr/include/seqan -I third_party -I third_party \
<------>-o bowtie-build-s ebwt_build.cpp \
<------>ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp  bowtie_build_main.cpp \
<------>-lpthread.
In file included from blockwise_sa.h:13:0,
                 from ebwt.h:27,
                 from ebwt_build.cpp:11:
diff_sample.h: In member function 'void DifferenceCoverSample<T>::build()':
diff_sample.h:859:3: error: '_Context_LSS' was not declared in this scope
   _Context_LSS<TIndexOff> c;
   ^
diff_sample.h:859:25: error: expected primary-expression before '>' token
   _Context_LSS<TIndexOff> c;
                         ^
diff_sample.h:859:27: error: 'c' was not declared in this scope
   _Context_LSS<TIndexOff> c;
                           ^
Makefile:205: recipe for target 'bowtie-build-s' failed
make[2]: *** [bowtie-build-s] Error 1
...


We have applied several patches which can be inspected in

   svn://anonscm.debian.org/debian-med/trunk/packages/bowtie/trunk/


Any help would be welcome

      Andreas.


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