Merge pull request #35 from broadinstitute/dp-mm2-empty-fix

minimap2 empty input bugfix
broadinstitute · Jun 23, 2020 · ad87de5 · ad87de5
2 parents fa37a9f + 4602149
commit ad87de5
Showing 1 changed file with 1 addition and 2 deletions.
diff --git a/tools/minimap2.py b/tools/minimap2.py
@@ -182,8 +182,7 @@ def align_one_rg(self, inBam, refDb, outBam, rgid=None, preset=None, options=Non
         # perform actual alignment
         if samtools.isEmpty(one_rg_inBam):
             # minimap doesn't like empty inputs, so copy empty bam through
-            outBam = one_rg_inBam
-            removeInput = False
+            samtools.sort(one_rg_inBam, outBam)
         else:
             self.align_cmd(one_rg_inBam, refDb, outBam, options=options, threads=threads)