Fix issue with targeted cov calculation

rulixxx · Aug 11, 2023 · 9e0bde8 · 9e0bde8
1 parent 3c3999b
commit 9e0bde8
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/python/runNanoSeq.py b/python/runNanoSeq.py
@@ -728,17 +728,17 @@ def vcfHeader(args):
                 iiresult.append(ifrag)
         gIntervals = iiresult
 
-        # correct total coverage (cctotal) if there are excluded regions
+        # correct total coverage (cctotal)
         xSumCov = 0
-        for iinterval in xIntervals:
+        for iinterval in gIntervals:
             ichar = iinterval.chr
             ibeg = iinterval.beg - 1
             iend = iinterval.end - 1
             for i in range(math.floor(ibeg/oargs['win']), math.floor(iend/oargs['win']) + 1):
                 if ( not ichar in chrOffset ) : break
                 j = i + chrOffset[ichar]
                 xSumCov += coverage[j][1]
-        cctotal = cctotal - xSumCov
+        cctotal = xSumCov
 
     # determine the genomic intervals to give to each job so that each one roughly
     # has the same amount of coverage