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Solving the issue of ZeroDivisionError #358

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Solving the issue of ZeroDivisionError #358

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2fb0df9
Solving the issue of ZeroDivisionError
mealser Oct 6, 2022
0d61c2d
Solving the issue of ZeroDivisionError
mealser Oct 6, 2022
096b5a0
Merge pull request #1 from mealser/patch-2
mealser Oct 6, 2022
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5 changes: 3 additions & 2 deletions src/sniffles/consensus.py
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Original file line number Diff line number Diff line change
Expand Up @@ -354,8 +354,9 @@ def novel_from_reads(best_lead,other_leads,klen,skip,skip_repetitive,debug=False
conseq_new.append("-"*len(buffer))
conseq="".join(conseq_new)

if span/float(len(best_lead.seq)) > minspan:
alignments.append(conseq)
if float(len(best_lead.seq))>0 :
if span/float(len(best_lead.seq)) > minspan:
alignments.append(conseq)

maxal=1
for i in range(len(best_lead.seq)):
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14 changes: 8 additions & 6 deletions src/sniffles/postprocessing.py
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Expand Up @@ -170,15 +170,17 @@ def qc_sv(svcall,config):
if stdev_pos > config.qc_stdev_abs_max:
svcall.filter="STDEV_POS"
return False
if svcall.svtype!="BND" and stdev_pos / abs(svcall.svlen) > 2.0:
svcall.filter="STDEV_POS"
return False
if abs(svcall.svlen)>0:
if svcall.svtype!="BND" and stdev_pos / abs(svcall.svlen) > 2.0:
svcall.filter="STDEV_POS"
return False

stdev_len = svcall.get_info("STDEV_LEN")
if stdev_len != None:
if svcall.svtype != "BND" and stdev_len / abs(svcall.svlen) > 1.0:
svcall.filter="STDEV_LEN"
return False
if abs(svcall.svlen)>0:
if svcall.svtype != "BND" and stdev_len / abs(svcall.svlen) > 1.0:
svcall.filter="STDEV_LEN"
return False
if stdev_len > config.qc_stdev_abs_max:
svcall.filter="STDEV_LEN"
return False
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