do not check for chromosome names in bam_is_sorted (#898)

set check_sq=False when opening a bam file in bam_is_sorted so we do not require chromosome names to be present
broadinstitute · Nov 27, 2018 · 5dbd9fc · 5dbd9fc
1 parent b546eae
commit 5dbd9fc
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/util/file.py b/util/file.py
@@ -500,7 +500,7 @@ def makeFastaFile(seqs, outFasta):
 
 def bam_is_sorted(bam_file_path):
     # Should perhaps be in samtools.py once it moves to pysam
-    samfile = pysam.AlignmentFile(bam_file_path, "rb")
+    samfile = pysam.AlignmentFile(bam_file_path, "rb", check_sq=False)
     if "HD" in samfile.header and "SO" in samfile.header["HD"]:
         return samfile.header["HD"]["SO"] in ("coordinate") # also: "queryname"
     else: