Package: bowtie / 1.2.3+dfsg-2

Metadata

Package Version Patches format
bowtie 1.2.3+dfsg-2 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
2to3.patch | (download)

bowtie | 2 1 + 1 - 0 !
bowtie-build | 2 1 + 1 - 0 !
bowtie-inspect | 2 1 + 1 - 0 !
scripts/test/btdata.py | 10 5 + 5 - 0 !
scripts/test/btface.py | 2 1 + 1 - 0 !
scripts/test/build_big.py | 6 3 + 3 - 0 !
scripts/test/dataface.py | 4 2 + 2 - 0 !
scripts/test/large_idx.py | 6 3 + 3 - 0 !
8 files changed, 17 insertions(+), 17 deletions(-)

 update python scripts to use python3
strip_html5shiv.patch | (download)

doc/manual.html | 3 0 + 3 - 0 !
1 file changed, 3 deletions(-)

 strip ie related condition to make lintian happy
 we don't care about ancient versions of IE
spelling.patch | (download)

MANUAL | 2 1 + 1 - 0 !
MANUAL.markdown | 2 1 + 1 - 0 !
doc/manual.html | 2 1 + 1 - 0 !
doc/website/manual.ssi | 4 2 + 2 - 0 !
ref_read.cpp | 2 1 + 1 - 0 !
5 files changed, 6 insertions(+), 6 deletions(-)

 fix spelling

no_hash_style_both_for_mips.patch | (download)

Makefile | 4 3 + 1 - 0 !
1 file changed, 3 insertions(+), 1 deletion(-)

 no_hash_style_both_for_mips
 cription: Disable -Wl,--hash-style=both on mips machines.
  It's not supported on mips and mipsel ports and leads to build errors.
use dpkg buildflags.patch | (download)

Makefile | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 use build flags from environment (dpkg-buildflags).
 Necessary for hardening flags.
use_debian_seqan.patch | (download)

Makefile | 3 1 + 2 - 0 !
1 file changed, 1 insertion(+), 2 deletions(-)

 use debian packaged seqan library instead of copy in upstream source
seqan fix setBegin call.patch | (download)

pat.h | 14 7 + 7 - 0 !
1 file changed, 7 insertions(+), 7 deletions(-)

 proper type-casting in using seqan::_setbegin().
 Required by newer versions of GCC.
seqan rename ChunkPool.patch | (download)

aligner.h | 12 6 + 6 - 0 !
aligner_0mm.h | 8 4 + 4 - 0 !
aligner_1mm.h | 8 4 + 4 - 0 !
aligner_23mm.h | 8 4 + 4 - 0 !
aligner_seed_mm.h | 8 4 + 4 - 0 !
ebwt_search.cpp | 12 6 + 6 - 0 !
ebwt_search_backtrack.h | 6 3 + 3 - 0 !
pool.h | 12 6 + 6 - 0 !
range_source.h | 6 3 + 3 - 0 !
9 files changed, 40 insertions(+), 40 deletions(-)

 renamed chunkpool class to bowtiechunkpool.
 SeqAn has a class with the same name and fatal name collision happens.
seqan rename fill to resize.patch | (download)

blockwise_sa.h | 8 4 + 4 - 0 !
diff_sample.h | 10 5 + 5 - 0 !
2 files changed, 9 insertions(+), 9 deletions(-)

 renamed seqan::fill function calls to use seqan::resize.
 SeqAn 1.3 renamed seqan::fill() to seqan::resize().
 SeqAn ticket: http://trac.seqan.de/ticket/77
disable_bits_flag.patch | (download)

Makefile | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 disable architecture bits detection.
 In Debian, you can use multiarch facilities for choosing which version 
 to run.
seqan popcount.patch | (download)

diff_sample.h | 3 3 + 0 - 0 !
1 file changed, 3 insertions(+)

 use seqan 1.4's seqan::popcount() function instead of own function
bowtie_ContextLss 1.1 1.4.patch | (download)

diff_sample.h | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 change class name of _context_lss
ppc64el.patch | (download)

Makefile | 14 7 + 7 - 0 !
1 file changed, 7 insertions(+), 7 deletions(-)

 enable for ppc64el
Bug-Debian: https://bugs.debian.org/788537
enable_arm64.patch | (download)

Makefile | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 enable arm64 architecture
 Forwarded-Upstream: yes (http://bugs.debian.org/800548)
Bug-Debian: https://bugs.debian.org/800548
reproducible.patch | (download)

Makefile | 10 5 + 5 - 0 !
1 file changed, 5 insertions(+), 5 deletions(-)

 make build reproducible
gcc 64bit.patch | (download)

Makefile | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 use gcc to determine if an arch is 64-bit
 uname -m is misleading when determining if an arch is 64-bit or not
 - It indicates the _build_ machine's processor which may not be the same as the
   processor the code is being built for (cross compiling).
 - It fails if a 32-bit compiler is used on a 64-bit cpu (eg build i386 packages
   on x86_64). This is common on the mips buildds.
 Therefore ask GCC if this architecture is 64-bit. Using __LP64__ is the easiest
 method, but is not portable and probably only works with GCC and Clang
 unfortunately.
build as Cpp03.patch | (download)

Makefile | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 build as c++03