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}
padding = 0
if record.INFO['SVTYPE'] == "DEL":
padding = spacerLength
for s2, e2 in sv[record.CHROM].overlap((max(s1 - padding, 0), e1 + padding)):
for inv3to3 in svDups[(record.CHROM, s2, e2)] + [sv[record.CHROM][(s2, e2)]]:
if inv3to3['id'] == record.ID:
continue
spacer = min(abs(e1-s2), abs(e2-s1))
(recO, nestedO, recUnion, bpOffset, oLen) = overlapMetrics((s1, e1), (s2, e2))
cc = carrierConcordance(nonRefHap, inv3to3['nonRefHap'])
delLength = min(e1-s1, e2-s2)
if record.INFO['SVTYPE'] == "INV":
delLength = min(max(s1,s2)-min(s1,s2), max(e1,e2)-min(e1,e2))
if (spacer <= spacerLength) and (cc >= minCarrierConcordance) and (min(spacer, delLength) >= deletionLength) and (recO <= maxReciprocalOverlap):
svControlID1 = re.sub(r"^[A-Z0]*","", record.ID)
rdRatio1 = 1.0
if int(svControlID1) in control.keys():
rdRatio1 = altRefReadDepthRatio(rc, control[int(svControlID1)], hap)
svControlID2 = re.sub(r"^[A-Z0]*","", inv3to3['id'])
rdRatio2 = 1.0
if int(svControlID2) in control.keys():
rdRatio2 = altRefReadDepthRatio(inv3to3['rc'], control[int(svControlID2)], inv3to3['hap'])
print(record.CHROM, record.POS, record.INFO['END'], record.ID, record.CHROM, s2, e2, inv3to3['id'], spacer, delLength, cc, rdRatio1, rdRatio2)
if (not args.readDepth) or ((rdRatio1<0.8) and (rdRatio2<0.8)):
score = float(min(peCount, inv3to3['pe'])) * float(cc)
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}
padding = 0
if record.INFO['SVTYPE'] == "DEL":
padding = spacerLength
for s2, e2 in sv[record.CHROM].overlap((max(s1 - padding, 0), e1 + padding)):
for inv3to3 in svDups[(record.CHROM, s2, e2)] + [sv[record.CHROM][(s2, e2)]]:
if inv3to3['id'] == record.ID:
continue
spacer = min(abs(e1-s2), abs(e2-s1))
(recO, nestedO, recUnion, bpOffset, oLen) = overlapMetrics((s1, e1), (s2, e2))
cc = carrierConcordance(nonRefHap, inv3to3['nonRefHap'])
delLength = min(e1-s1, e2-s2)
if record.INFO['SVTYPE'] == "INV":
delLength = min(max(s1,s2)-min(s1,s2), max(e1,e2)-min(e1,e2))
if (spacer <= spacerLength) and (cc >= minCarrierConcordance) and (min(spacer, delLength) >= deletionLength) and (recO <= maxReciprocalOverlap):
svControlID1 = re.sub(r"^[A-Z0]*","", record.ID)
rdRatio1 = 1.0
if int(svControlID1) in control.keys():
rdRatio1 = altRefReadDepthRatio(rc, control[int(svControlID1)], hap)
svControlID2 = re.sub(r"^[A-Z0]*","", inv3to3['id'])
rdRatio2 = 1.0
if int(svControlID2) in control.keys():
rdRatio2 = altRefReadDepthRatio(inv3to3['rc'], control[int(svControlID2)], inv3to3['hap'])
print(record.CHROM, record.POS, record.INFO['END'], record.ID, record.CHROM, s2, e2, inv3to3['id'], spacer, delLength, cc, rdRatio1, rdRatio2)
if (not args.readDepth) or ((rdRatio1<0.8) and (rdRatio2<0.8)):
score = float(min(peCount, inv3to3['pe'])) * float(cc)
if (call.called) and (call.sample in sampleSet):
rc[call.sample] = call['RC']
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']
dupInfo = {'id': "NA", 'start': 0, 'end': 0, 'score': -1}
for s2, e2 in sv[record.CHROM].overlap((s1, e1)):
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)
G.add_node((record.ID, dupInfo['id']))
G.node[(record.ID, dupInfo['id'])]['Score'] = dupInfo['score']
for dupIStart, dupIEnd in dupRegion[record.CHROM].overlap((dupInfo['start'], dupInfo['end'])):
(id1, id2) = dupRegion[record.CHROM][(dupIStart, dupIEnd)]
if overlapValid((dupInfo['start'], dupInfo['end']), (dupIStart, dupIEnd), 0.1, 10000):
G.add_edge((record.ID, dupInfo['id']), (id1, id2))
int(gVal) for gVal in call['GT'].split('/')
]
peCount += call['DV']
if len(nonRefHap):
# Collect overlapping calls
s1 = record.POS
e1 = record.INFO['END']
dupInfo = {'id': "NA", 'start': 0, 'end': 0, 'score': -1}
for s2, e2 in sv[record.CHROM].overlap((s1, e1)):
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'],
support += call["RV"]
else:
if call["DV"] >= 2:
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"]:
