Update by asebastian on Mon Nov 13 15:00:14 EST 2017 from Aswathys-iMac.local
@@ -4,6 +4,10 @@ import sys, csv , re
import csv
+def get_factor():
+ return 1
+
+
def parse_idxstats(fname):
'''
parse samtools idxstats results and returns a list of (tag,value) pair.
@@ -21,7 +25,8 @@ def parse_idxstats(fname):
elem = store[sample]
name, size, mapped, unmapped = row
- elem.setdefault(name, []).append((int(size), int(mapped)))
+ mapped_cov = mapped * get_factor()
+ elem.setdefault(name, []).append((int(size), int(mapped_cov)))
return store
