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, 16 insertions, 0 deletions
diff --git a/sci-biology/reapr/files/fix_sort_samtools13.patch b/sci-biology/reapr/files/fix_sort_samtools13.patch new file mode 100644 index 000000000..f009223ce --- /dev/null +++ b/sci-biology/reapr/files/fix_sort_samtools13.patch @@ -0,0 +1,16 @@ +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"; |