psudmant / ssf_dts_caller Goto Github PK

Hi，Would you like to share the python module wssd-pw-common ?I can't run these scripts without wssd-pw-common .Thanks

line 440 in genotyper.py:
CNV_segs[-1][1] = e

If CNV_segs is an empty list, an IndexError will be returned.
A simple fix would be to add these lines:

if CNV_segs == []:
    CNV_segs.append([s,e])
else:
    CNV_segs[-1][1] = e

Or use a ternary operator:
CNV_segs[-1][1] = e if CNV_segs != [] else CNV_segs.append([s,e])

• merge segments in a block based the actual copy of the adjacent segments, not the total copy of all segments
• output genotypes of ALL regions for overlapping duplicated loci, assuming not massively overlapping
• some filtering is still probably needed for singletons and dups in some individuals