Disable flagstat test as output differs in samtools-1.13
@@ -244,7 +244,8 @@ class SamtoolsTest(unittest.TestCase):
command = self.get_command(statement, map_to_internal=False)
# bam2fq differs between version 1.5 and 1.6 - re-enable if
# bioconda samtools will be available.
- if command in ("bedcov", "stats", "dict", "bam2fq"):
+ # flagstat differs between version <=1.12 and >=1.13
+ if command in ("bedcov", "stats", "dict", "bam2fq", "flagstat"):
continue
if (command == "calmd" and
