Commit d50e14ee authored by bow's avatar bow
Browse files

Add fix_mpileup.py script for VarScan

parent bf8743a5
#!/usr/bin/env python
from __future__ import print_function
__author__="Wai Yi Leung"
import sys
if __name__ == "__main__":
"""
Fix the mpileupformat for RNA mpileup
Solution offered by Irina Pulyakhina (LUMC-HG)
http://www.biostars.org/p/78542/
"""
for line in sys.stdin:
l = line.strip().split("\t")
if l[3] == "0":
# no alignment to this position
print("\t".join(map(str, l)))
continue
fix_col = l[4].replace('<', '').replace('>', '')
new_size = len(fix_col)
old_size = len(l[4])
if new_size != old_size:
l[4] = fix_col
l[3] = "{}".format(new_size)
if new_size == 0:
l[5] = ""
print("\t".join(map(str, l)))
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