Package: bowtie / 1.1.1-2

Metadata

Package Version Patches format
bowtie 1.1.1-2 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
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 | 26 13 + 13 - 0 !
1 file changed, 13 insertions(+), 13 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.
no_hash_style_both_for_mips.patch | (download)

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

 disable -wl,--hash-style=both on mips machines.
 It's not supported on mips and mipsel ports and leads to build errors.
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