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pylint fix
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ACEnglish committed Jan 5, 2025
1 parent e8b15b6 commit f46c121
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2 changes: 1 addition & 1 deletion truvari/collapse.py
Original file line number Diff line number Diff line change
Expand Up @@ -723,7 +723,7 @@ def dump_log(self):

class LinkedList:
"""
Simple linked list which should(?) be faster than concatenating a bunch
Simple linked list which should(?) be faster than concatenating a bunch
regular lists
"""
def __init__(self, data=None):
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8 changes: 4 additions & 4 deletions truvari/matching.py
Original file line number Diff line number Diff line change
Expand Up @@ -265,12 +265,12 @@ def bnd_build_match(self, base, comp, matid=None, **_kwargs):
"""
def bounds(pos):
"""
Inflate a bnd position based on CIPOS.
Inflate a bnd position based on CIPOS.
Experimental, but it's getting tricky, so need clarification
For example, why does GIAB use CIPOS1 instead of the standard CIPOS? (not to mention Type=String).
Also, I assumed that the CIPOS was ±POS, but it seems like the standard is that the ambiguity is between
POS, POS+CIPOS[0]. But then, there is no enforcement of strands with CIPOS, I think, so it could always be
positive and if it's a complement BND it might need POS - CIPOS?
Also, I assumed that the CIPOS was ±POS, but it seems like the standard is that the ambiguity is between
POS, POS+CIPOS[0]. But then, there is no enforcement of strands with CIPOS, I think, so it could always be
positive and if it's a complement BND it might need POS - CIPOS?
I'm dropping for now
entry and key were also parameters
key = 'CI' + key
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