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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";
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