Ignore unmapped reads when reading input file - #68

guigolab · Aug 2, 2021 · 39c5826 · 39c5826
1 parent dc1b10c
commit 39c5826
Showing 1 changed file with 6 additions and 2 deletions.
diff --git a/ggsashimi.py b/ggsashimi.py
@@ -168,11 +168,15 @@ def read_bam(f, c, s):
         if s != "NONE":
                 a["-"] = [0] * (end - start)
                 junctions["-"] = OrderedDict()
-        
+
         samfile = pysam.AlignmentFile(f)
 
         for read in samfile.fetch(chr, start, end):
-
+
+                # Move forward if read is unmapped
+                if read.is_unmapped:
+                    continue
+
                 samflag, read_start, CIGAR = read.flag, read.reference_start+1, read.cigarstring
 
                 # Ignore reads with more exotic CIGAR operators