def parse_breakend(record1, record2, datahub):
result1 = _parse_breakend(record1)
result2 = _parse_breakend(record2)
if not (result1["chrom"] == result2["other_chrom"]
and result1["pos"] == result2["other_pos"]):
print(result1)
print(result2)
logger.error(
"Malformed VCF: breakends do not appear to match:\n{}\n{}".format(
record1, record2))
return None
if result1["chrom"] == result1["other_chrom"] and \
abs(result1["pos"]-result1["other_pos"]) < datahub.align_distance*5:
logger.error("Can't yet handle nearby breakends; skipping")
return None
# convert from 1-based to 0-based coordinates
breakpoint1 = Locus(result1["chrom"], result1["pos"] - 1,
result1["pos"] - 1, result1["orientation"][0])
breakpoint2 = Locus(result1["other_chrom"], result1["other_pos"] - 1,
result1["other_pos"] - 1, result1["orientation"][1])
# print(breakpoint1, breakpoint2)
return variants.Breakend(breakpoint1, breakpoint2, datahub, result1["id"])
def get_translocation(record, datahub):
breakpoint1 = Locus(record.chrom, record.start, record.start, "+")
breakpoint2 = Locus(record.info["CHR2"], record.end, record.end,
"+" if record.info["STRAND"] == "+" else "-")
variants.Breakend(breakpoint1, breakpoint2, datahub, record.id)
raise NotImplementedError()