diff options
Diffstat (limited to 'sci-biology/reapr/files/fix_sort_samtools13.patch')
| -rw-r--r-- | sci-biology/reapr/files/fix_sort_samtools13.patch | 16 |
1 files changed, 0 insertions, 16 deletions
diff --git a/sci-biology/reapr/files/fix_sort_samtools13.patch b/sci-biology/reapr/files/fix_sort_samtools13.patch deleted file mode 100644 index f009223ce..000000000 --- a/sci-biology/reapr/files/fix_sort_samtools13.patch +++ /dev/null @@ -1,16 +0,0 @@ -Description: adapt samtools sort usage to 1.3 syntax - Samtools 1.3 changed the syntax of the 'samtools sort' command, breaking - REAPR's smaltmap command in the process. - Discussed and forwarded to upstream in person, hence no URL. -Author: Sascha Steinbiss <sascha@steinbiss.name> ---- a/src/task_smaltmap.pl -+++ b/src/task_smaltmap.pl -@@ -155,7 +155,7 @@ - . " | $samtools view -S -T $assembly -b - > $raw_bam"; - - # sort the bam by coordinate --push @commands, "$samtools sort $raw_bam $raw_bam.sort"; -+push @commands, "$samtools sort $raw_bam -O bam -o $raw_bam.sort.bam"; - - # remove duplicates - push @commands, "$samtools rmdup $raw_bam.sort.bam $rmdup_bam"; |