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";