prefix arg was depricated and completely removed in samtools sort 1.3…

…, so let's use '-T' option for it
iromeo · Jan 29, 2016 · c45210d · c45210d
1 parent 1344eba
commit c45210d
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/bwameth.py b/bwameth.py
@@ -206,7 +206,7 @@ def as_bam(pfile, fa, prefix, calmd=False, set_as_failed=None):
     set_as_failed: None, 'f', or 'r'. If 'f'. Reads mapping to that strand
                       are given the sam flag of a failed QC alignment (0x200).
     """
-    view = "samtools view -bS - | samtools sort -m 2415919104 - "
+    view = "samtools view -bS - | samtools sort -m 2415919104 - -T "
     if calmd:
         cmds = [
             view + "{bam}.tmp",