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Updates to vcf_mod.py to fix the RPA annotation #17

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Merged
DonFreed merged 2 commits into from
Nov 28, 2025
Merged

Updates to vcf_mod.py to fix the RPA annotation #17

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f9c8811
Update `vcf_mod.py` to skip annotations with incorrect lengths
DonFreed Oct 9, 2025
fdc2556
Updates to vcf_mod.py
DonFreed Nov 28, 2025
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39 changes: 20 additions & 19 deletions sentieon_cli/scripts/vcf_mod.py
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Original file line number Diff line number Diff line change
Expand Up @@ -623,30 +623,31 @@ def join2(f0, f1, f2, v0, v1, v2, pos, bed):
continue
elif t == 'R':
if k == 'RPA':
d0 = d1 = d2 = [-1] * (len(v.alt)+1)
if v0 and v0.info.get(k):
s = v0.info.get(k)
d0 = [i >= 0 and s[i] or -1 for i in m0]
if v1 and v1.info.get(k):
d1 = d2 = [-1] * (len(v.alt)+1)
if i1 > 0 and v1.info.get(k):
s = v1.info.get(k)
d1 = [i >= 0 and s[i] or -1 for i in m1]
if v2 and v2.info.get(k):
if i2 > 0 and v2.info.get(k):
s = v2.info.get(k)
d2 = [i >= 0 and s[i] or -1 for i in m2]
d = [max(e) for e in zip(d0,d1,d2)]
d = [max(e) for e in zip(d1,d2)]
if min(d) > 0:
v.info[k] = d
continue
continue
else:
if k in ('STR', 'RU'):
d = None
d = d and d or v1 and v1.info.get(k)
d = d and d or v2 and v2.info.get(k)
d = d and d or v0 and v0.info.get(k)
if d:
if i1 > 0 and i2 > 0 and v1.info.get(k) == v2.info.get(k):
d = v1.info.get(k)
elif i1 > 0:
d = v1.info.get(k)
elif i2 > 0:
d = v2.info.get(k)
else:
d = None
if d is not None:
v.info[k] = d
continue
if k == 'DP':
continue
elif k == 'DP':
d = -1
if d < 0 and v0:
d = v0.info.get(k, -1)
Expand All @@ -656,15 +657,15 @@ def join2(f0, f1, f2, v0, v1, v2, pos, bed):
d += v2 and v2.info.get(k, 0) or 0
if d >= 0:
v.info[k] = d
continue
if k == 'ML_PROB':
continue
elif k == 'ML_PROB':
d = (u.info.get(k) for u in (v1,v2) if u)
d = [e for e in d if e is not None]
if d:
d = functools.reduce(operator.mul, d, 1)
v.info[k] = round(d, 2)
continue
if k not in ('QD',):
continue
elif k not in ('QD',):
continue
v.info.pop(k, None)

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