1 files changed, 0 insertions, 40 deletions
diff --git a/sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch
deleted file mode 100644
index cb7dfb08a..000000000
--- a/sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-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
-