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modify on pos2, add compatibility to indel recs #2

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modify on pos2, add compatibility to indel recs #2

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9 changes: 6 additions & 3 deletions mergesvvcf/mergedfile.py
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Original file line number Diff line number Diff line change
Expand Up @@ -197,9 +197,12 @@ def passed_variant(record):
formats = []
for hformat in vcf_reader.header.formats.itervalues():
num = None
if hformat.name == "GT" or hformat.number == "G":
num = "G"
continue # Genotype is special cant do multiple
# if hformat.name == "GT" or hformat.number == "G":
# num = "G"
# continue # Genotype is special cant do multiple
if hformat.name == "PL": num = "G"
if hformat.number == "G": num = "G"
if hformat.name == "GL": num = "3"
outvcf.header.formats.add(
"{}_{}".format(program, hformat.name),
num or hformat.number,
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6 changes: 4 additions & 2 deletions mergesvvcf/vcftobreakpoints.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -155,8 +155,10 @@ def breakpointsFromRecord(record):
# defaults
if chr2 is None:
chr2 = chr1
if pos2 is None and "<" in altstr:
if pos2 is None and "<" in altstr and ">" in altstr:
pos2 = record.stop
elif pos2 is None and re.match(r'^[ATCG]+$', altstr.strip(".")):
pos2 = record.pos + len(altstr.strip("."))

# look for symbolic SVTYPE information in the alt field (eg, <DEL>)
resultSym = re.match(__symbolicRE__, altstr)
Expand Down Expand Up @@ -189,7 +191,7 @@ def breakpointsFromRecord(record):

reflen = len(ref)
if pos2 is None:
pos2 = pos1 + reflen
pos2 = pos1 + len(altstr.strip("."))
if svlen is None:
svlen = len(altstr) - reflen
if svtype is None:
Expand Down