Merge pull request #151 from ajank/master

Fix handling chimeric alignments in hicBuildMatrix

hicexplorer/hicBuildMatrix.py

@@ -5,6 +5,7 @@
 import time
 from os import unlink
 import os
+import itertools
 
 import pysam
 from six.moves import xrange
@@ -475,7 +476,7 @@ def get_supplementary_alignment(read, pysam_obj):
         supplementary_alignment = []
         for i in range(len(other_alignments)):
             _sup = pysam_obj.next()
-            if _sup.is_supplementary and _sup.qname == read.qname:
+            if _sup.qname == read.qname:
                 supplementary_alignment.append(_sup)
 
         return supplementary_alignment
@@ -529,8 +530,11 @@ def get_correct_map(primary, supplement_list):
         else:
             cigartuples = read.cigartuples[:]
 
+        # For each read in read_list, calculate the position of the first match (operation M in CIGAR string) in the read sequence.
+        # The calculation is done by adding up the lengths of all the operations until the first match.
+        # CIGAR string is a list of tuples of (operation, length). Match is stored as CMATCH.
         first_mapped.append(
-            [x for x, cig in enumerate(cigartuples) if cig[0] == 0][0])
+            sum(count for op, count in itertools.takewhile(lambda (op, count): op != pysam.CMATCH, cigartuples)))
     # find which read has a cigar string that maps first than any of the
     # others.
     idx_min = first_mapped.index(min(first_mapped))