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author | David Seifert <soap@gentoo.org> | 2016-04-03 19:57:05 +0200 |
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committer | David Seifert <soap@gentoo.org> | 2016-04-03 19:57:05 +0200 |
commit | f462f85a318159798956f27b851268e7fd0c2a16 (patch) | |
tree | d01a9e4c242f1c71f54a9f868be1e5b76517f000 /sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch | |
parent | media-libs/qt-gstreamer: Fix BOOST_JOIN with >=dev-libs/boost-1.60.0 (diff) | |
download | gentoo-f462f85a318159798956f27b851268e7fd0c2a16.tar.gz gentoo-f462f85a318159798956f27b851268e7fd0c2a16.tar.bz2 gentoo-f462f85a318159798956f27b851268e7fd0c2a16.zip |
sci-biology/abyss: Latest ebuild from science-overlay
* EAPI=6
Package-Manager: portage-2.2.28
Diffstat (limited to 'sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch')
-rw-r--r-- | sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch | 40 |
1 files changed, 40 insertions, 0 deletions
diff --git a/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch new file mode 100644 index 000000000000..cb7dfb08a84d --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch @@ -0,0 +1,40 @@ +Hello, + +I see Shaun Jackmans' (abyss-)sam2afg script is available within the +Amos source repository. I find this very useful for coercing output from +assemblers which which don't track read location into amos by remapping +reads against the assembly and converting to afg - not ideal but better +than nothing when you don't have the 'real' read locations to work with. + +This fails, however when reads are aligned with 'bwa mem', which can +output multi-part alignments. sam2afg checks for reuse of the same read +id (presumably to prevent the generation of non-unique eid values), +consequently encountering multiple alignments for a read causes it to die. + +The following one-line patch allows sam2afg to skip these secondary +alignments present in 'bwa mem' output, provided bwa mem has been run +with the '-M' argument which sets the SAM 'secondary alignment' flag on +the alignments in question. + +Hopefully this will also be of use to others... + +Best Regards, +James + +-- +Dr. James Abbott +Lead Bioinformatician +Bioinformatics Support Service +Imperial College, London + + +--- abyss-1.3.6/bin/abyss-samtoafg.ori 2015-05-23 23:43:46.797747928 +0200 ++++ abyss-1.3.6/bin/abyss-samtoafg 2015-05-23 23:44:09.227747743 +0200 +@@ -105,6 +105,7 @@ + die unless defined $qqual; + + $tstart--; # convert to zero-based coordinate ++ next if $flag & 0x100; # secondary alignment + $qid .= "/1" if $flag & 0x40; #FREAD1 + $qid .= "/2" if $flag & 0x80; #FREAD2 + |