for dup5to3 in svDups[(record.CHROM, s2,
e2)] + [sv[record.CHROM][(s2, e2)]]:
(recO, nestedO, recUnion, bpOffset,
oLen) = overlapMetrics((s1, e1), (s2, e2))
minBpOffset = min(abs(s2 - s1), abs(e2 - e1))
maxBpOffset = max(abs(s2 - s1), abs(e2 - e1))
cc = carrierConcordance(nonRefHap, dup5to3['hap'])
if (nestedO >= minNestedOverlap) and (
minBpOffset < maxInsertionOffset) and (
maxBpOffset > minDuplicationLength) and (
cc >= minCarrierConcordance):
rdRatio = rdAltRefRatio(
((s1, e1), (s2, e2)),
(nonRefHap, dup5to3['hap']),
(rc, dup5to3['rc']))
if validRdRatio(recO / nestedO, rdRatio,
args.readDepth)[0]:
score = float(min(peCount,
dup5to3['pe'])) * float(cc)
if score > dupInfo['score']:
dupInfo = {
'id': dup5to3['id'],
'start': min(s1, s2),
'end': max(e1, e2),
'score': score
}
if dupInfo['score'] >= 0:
if not dupRegion.has_key(record.CHROM):
dupRegion[record.CHROM] = banyan.SortedDict(
key_type=(int, int),
alg=banyan.RED_BLACK_TREE,
updator=banyan.OverlappingIntervalsUpdator)
nonRefHap[call.sample] = [int(gVal) for gVal in call['GT'].split('/')]
support += call['DV']
if len(nonRefHap):
# Collect overlapping calls
s1 = record.POS
e1 = record.INFO['END']
invInfo = {'id': "NA", 'start': 0, 'end': 0, 'score': -1}
for s2, e2 in sv[record.CHROM].overlap((s1, e1)):
for inv3to3 in svDups[(record.CHROM, s2, e2)] + [sv[record.CHROM][(s2, e2)]]:
(recO, nestedO, recUnion, bpOffset, oLen) = overlapMetrics((s1, e1), (s2, e2))
minBpOffset = min(abs(s2-s1), abs(e2-e1))
maxBpOffset = max(abs(s2-s1), abs(e2-e1))
cc = carrierConcordance(nonRefHap, inv3to3['hap'])
if (nestedO >= minNestedOverlap) and (minBpOffset < maxInsertionOffset) and (cc >= minCarrierConcordance):
rdRatio = rdAltRefRatio(((s1, e1), (s2, e2)), (nonRefHap, inv3to3['hap']), (rc, inv3to3['rc']))
valid, updSVType = validRdRatio(recO/nestedO, rdRatio)
if valid:
if (record.INFO['SVTYPE'] != 'INV') and (updSVType != "DUP"):
continue
if (updSVType != 'DUP') or (maxBpOffset > minDuplicationLength):
score = float(min(support, inv3to3['sup'])) * float(cc)
if score > invInfo['score']:
invInfo = {'id': inv3to3['id'], 'start': min(s1, s2), 'end': max(e1, e2), 'score': score}
if invInfo['score'] >= 0:
if not invRegion.has_key(record.CHROM):
invRegion[record.CHROM] = banyan.SortedDict(key_type=(int, int), alg=banyan.RED_BLACK_TREE, updator=banyan.OverlappingIntervalsUpdator)
G.add_node((record.ID, invInfo['id']))
G.node[(record.ID, invInfo['id'])]['Score'] = invInfo['score']
for invIStart, invIEnd in invRegion[record.CHROM].overlap((invInfo['start'], invInfo['end'])):
(id1, id2) = invRegion[record.CHROM][(invIStart, invIEnd)]
if overlapValid((invInfo['start'], invInfo['end']), (invIStart, invIEnd), 0.1, 10000):
if (call.gt_type != 0) and (call['DV'] > 0):
nonRefHap[call.sample] = [int(gVal) for gVal in call['GT'].split('/')]
peCount += call['DV']
if len(nonRefHap):
# Collect overlapping calls
s1 = record.POS
e1 = record.INFO['END']
invInfo = {'id': "NA", 'start': 0, 'end': 0, 'score': -1}
for s2, e2 in sv[record.CHROM].overlap((s1, e1)):
for inv3to3 in svDups[(record.CHROM, s2, e2)] + [sv[record.CHROM][(s2, e2)]]:
(recO, nestedO, recUnion, bpOffset, oLen) = overlapMetrics((s1, e1), (s2, e2))
minBpOffset = min(abs(s2-s1), abs(e2-e1))
cc = carrierConcordance(nonRefHap, inv3to3['hap'])
if (nestedO >= minNestedOverlap) and (minBpOffset < maxInsertionOffset) and (cc >= minCarrierConcordance):
rdRatio = rdAltRefRatio(((s1, e1), (s2, e2)), (nonRefHap, inv3to3['hap']), (rc, inv3to3['rc']))
if validRdRatio(recO/nestedO, rdRatio, args.readDepth)[0]:
score = float(min(peCount, inv3to3['pe'])) * float(cc)
if score > invInfo['score']:
invInfo = {'id': inv3to3['id'], 'start': min(s1, s2), 'end': max(e1, e2), 'score': score}
if invInfo['score'] >= 0:
if not invRegion.has_key(record.CHROM):
invRegion[record.CHROM] = banyan.SortedDict(key_type=(int, int), alg=banyan.RED_BLACK_TREE, updator=banyan.OverlappingIntervalsUpdator)
G.add_node((record.ID, invInfo['id']))
G.node[(record.ID, invInfo['id'])]['Score'] = invInfo['score']
for invIStart, invIEnd in invRegion[record.CHROM].overlap((invInfo['start'], invInfo['end'])):
(id1, id2) = invRegion[record.CHROM][(invIStart, invIEnd)]
if overlapValid((invInfo['start'], invInfo['end']), (invIStart, invIEnd), 0.1, 10000):
G.add_edge((record.ID, invInfo['id']), (id1, id2))
invRegion[record.CHROM][(invInfo['start'], invInfo['end'])] = (record.ID, invInfo['id'])
# Pick best pair of inversions out of all overlapping calls
for s2, e2 in sv[record.CHROM].overlap((s1, e1)):
for inv3to3 in svDups[(record.CHROM, s2,
e2)] + [sv[record.CHROM][(s2, e2)]]:
(recO, nestedO, recUnion, bpOffset,
oLen) = overlapMetrics((s1, e1), (s2, e2))
minBpOffset = min(abs(s2 - s1), abs(e2 - e1))
maxBpOffset = max(abs(s2 - s1), abs(e2 - e1))
cc = carrierConcordance(nonRefHap, inv3to3['hap'])
if (nestedO >= minNestedOverlap) and (
minBpOffset < maxInsertionOffset) and (
cc >= minCarrierConcordance):
rdRatio = rdAltRefRatio(
((s1, e1), (s2, e2)),
(nonRefHap, inv3to3['hap']),
(rc, inv3to3['rc']))
valid, updSVType = validRdRatio(
recO / nestedO, rdRatio)
if valid:
if (record.INFO['SVTYPE'] !=
'INV') and (updSVType != "DUP"):
continue
if (updSVType != 'DUP') or (
maxBpOffset > minDuplicationLength):
score = float(min(
support, inv3to3['sup'])) * float(cc)
if score > invInfo['score']:
invInfo = {
'id': inv3to3['id'],
'start': min(s1, s2),
'end': max(e1, e2),
'score': score
}
