Added code to skip commented lines so that AMULET can run on Cell Ranger

ATAC 2.0 fragment file outputs.
UcarLab · Sep 10, 2021 · f45d1c4 · f45d1c4
1 parent c4ecf9d
commit f45d1c4
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/FragmentFileOverlapCounter.py b/FragmentFileOverlapCounter.py
@@ -261,7 +261,12 @@ def findOverlaps(fragmentfile, singlecellfile, expectedoverlap, chrlist, path, m
         stats_readcount += 1
 
         decodedline = linedecoder(curline)
+
+        if decodedline.strip().startswith("#"):
+            continue
+
         split = decodedline.split("\t")
+
         curchr = split[0]
         curstart = int(split[1])+startbases
         curend = int(split[2])+endbases