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minor: small issue with museq_het

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Diljot Grewal
Diljot Grewal committed Jan 21, 2019
1 parent c88c2c3 commit c3f87b09e841e31fd75dff5abd9d92c5dc3232b3
Showing with 8 additions and 2 deletions.
  1. +8 −2 museq/preprocessutils.py
@@ -86,8 +86,14 @@ def get_features(self):
logging.error(str(position)+' position references base N and has been ignored')
continue

outstr = self._make_outstr(it, rt[0],tt)

# swapped tum and norm when calling outstr, so it returns the values on wrong index. swap them later
# we're using counts from normal to decide ref and alt, then grabbing counts for those in tumour
# normally its the other way around.
outstr = self._make_outstr(it, rt[0], tt)
normoutstr = outstr[-2]
tumoutstr = outstr[-1]
outstr[-2] = tumoutstr
outstr[-1] = normoutstr

if outstr[-1][5] == '0/1':
## calculate features

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