public static PairResult[] CollectIndelEvidence(IndelTargetFinder targetFinder, string chrom,
ConcurrentDictionary <string, IndelEvidence> indelLookup, PairResult[] pairs)
{
var localResult = new Dictionary <string, IndelEvidence>();
foreach (var p in pairs)
{
var MinMapQualityForEvidence = 10;
var pClassification = p.Classification;
if (p.HasIndels)
{
// Reputable indel reads will not have lots of mismatches or softclips
p.OriginalIndelsR1 = new List <PreIndel>();
p.OriginalIndelsR2 = new List <PreIndel>();
var stitched = pClassification == PairClassification.ImperfectStitched ||
pClassification == PairClassification.MessyStitched ||
pClassification == PairClassification.PerfectStitched ||
pClassification == PairClassification.SingleMismatchStitched;
// Assumes we're not ever dealing with stitched reads here
var aln = p.ReadPair.Read1;
if (aln != null && aln.IsMapped() && aln.RefID >= 0)
{
// TODO would anything ever be coming through here that is _not_ ClassificationContainsQualityIndels?
if (ClassificationContainsQualityIndels(pClassification))
{
p.OriginalIndelsR1 = IndelEvidenceHelper.FindIndelsAndRecordEvidence(aln, targetFinder, localResult,
p.IsReputableIndelContaining, chrom, MinMapQualityForEvidence, stitched);
}
}
aln = p.ReadPair.Read2;
if (aln != null && aln.IsMapped() && aln.RefID >= 0)
{
// TODO would anything ever be coming through here that is _not_ ClassificationContainsQualityIndels?
if (ClassificationContainsQualityIndels(pClassification))
{
p.OriginalIndelsR2 = IndelEvidenceHelper.FindIndelsAndRecordEvidence(aln, targetFinder, localResult,
p.IsReputableIndelContaining, chrom, MinMapQualityForEvidence, stitched);
}
}
}
}
foreach (var kvp in localResult)
{
indelLookup.AddOrUpdate(kvp.Key, kvp.Value, (k, v) =>
{
v.AddIndelEvidence(kvp.Value);
return(v);
});
}
return(pairs);
}
public void CollectEvidence(BamAlignment alignment, bool isReputable, bool isStitched, string chromosome)
{
IndelEvidenceHelper.FindIndelsAndRecordEvidence(alignment, _targetFinder, _lookup, isReputable, chromosome, 30, isStitched);
}
public void FindIndelsAndRecordEvidence()
{
var readPair = TestHelpers.GetPair("5M1D5M", "5M2I4M", nm2: 3);
var readPair2 = TestHelpers.GetPair("3M1D8M", "5M1D5M", nm2: 4);
var targetFinder = new IndelTargetFinder();
var lookup = new Dictionary <string, IndelEvidence>();
IndelEvidenceHelper.FindIndelsAndRecordEvidence(readPair.Read1, targetFinder, lookup, true, "chr1", 10);
var expectedDel = "chr1:104 NN>N";
var expectedIns = "chr1:104 N>NTT";
Assert.Equal(1.0, lookup.Count);
Assert.Equal(expectedDel, lookup.Keys.First());
//obs,left,right,mess,quals,fwd,reverse,stitched,reput
var evidence = new IndelEvidence()
{
Observations = 1,
LeftAnchor = 5,
RightAnchor = 5,
Mess = 0,
Quality = 30,
Forward = 1,
Reverse = 0,
Stitched = 0,
ReputableSupport = 1,
IsRepeat = 0,
IsSplit = 0
};
ValidateEvidenceMatches(evidence, lookup[expectedDel]);
// Build evidence for same indel, let's call it stitched this time
IndelEvidenceHelper.FindIndelsAndRecordEvidence(readPair.Read1, targetFinder, lookup, true, "chr1", 10, true);
Assert.Equal(1.0, lookup.Count);
Assert.Contains(expectedDel, lookup.Keys);
ValidateEvidenceMatches(new IndelEvidence()
{
Observations = 2,
LeftAnchor = 10,
RightAnchor = 10,
Mess = 0,
Quality = 60,
Forward = 1,
Reverse = 0,
Stitched = 1,
ReputableSupport = 2,
IsRepeat = 0,
IsSplit = 0
}, lookup[expectedDel]);
// Build evidence for same indel from a different read, this one's not reputable and is reverse
IndelEvidenceHelper.FindIndelsAndRecordEvidence(readPair2.Read2, targetFinder, lookup, false, "chr1", 10);
Assert.Equal(1.0, lookup.Count);
Assert.Contains(expectedDel, lookup.Keys);
// mess should subtract ins length from nm
ValidateEvidenceMatches(
new IndelEvidence()
{
Observations = 3,
LeftAnchor = 15,
RightAnchor = 15,
Mess = 3,
Quality = 90,
Forward = 1,
Reverse = 1,
Stitched = 1,
ReputableSupport = 2,
IsRepeat = 0,
IsSplit = 0
}, lookup[expectedDel]);
// Different indel, reverse only
IndelEvidenceHelper.FindIndelsAndRecordEvidence(readPair.Read2, targetFinder, lookup, true, "chr1", 10);
Assert.Equal(2, lookup.Count);
// Original del shouldn't have changed
Assert.Contains(expectedDel, lookup.Keys);
ValidateEvidenceMatches(
new IndelEvidence()
{
Observations = 3,
LeftAnchor = 15,
RightAnchor = 15,
Mess = 3,
Quality = 90,
Forward = 1,
Reverse = 1,
Stitched = 1,
ReputableSupport = 2,
IsRepeat = 0,
IsSplit = 0
}, lookup[expectedDel]);
Assert.Contains(expectedIns, lookup.Keys);
// mess should subtract ins length from nm
ValidateEvidenceMatches(
new IndelEvidence
{
Observations = 1,
LeftAnchor = 5,
RightAnchor = 4,
Mess = 1,
Quality = 30,
Forward = 0,
Reverse = 1,
Stitched = 0,
ReputableSupport = 1,
IsRepeat = 0,
IsSplit = 0
}
, lookup[expectedIns]);
// Multi-indel
var readPairMulti = TestHelpers.GetPair("5M1D1M1D4M", "5M1D1M1D4M", nm: 2, nm2: 2);
IndelEvidenceHelper.FindIndelsAndRecordEvidence(readPairMulti.Read1, targetFinder, lookup, true, "chr1", 10);
Assert.Equal(3, lookup.Count);
// Original del shouldn't have changed
Assert.Contains(expectedDel, lookup.Keys);
ValidateEvidenceMatches(
new IndelEvidence()
{
Observations = 3,
LeftAnchor = 15,
RightAnchor = 15,
Mess = 3,
Quality = 90,
Forward = 1,
Reverse = 1,
Stitched = 1,
ReputableSupport = 2,
IsRepeat = 0,
IsSplit = 0
}, lookup[expectedDel]);
var expectedMulti = "chr1:104 NN>N|chr1:106 NN>N";
Assert.Contains(expectedMulti, lookup.Keys);
ValidateEvidenceMatches(
new IndelEvidence()
{
Observations = 1,
LeftAnchor = 5,
RightAnchor = 4,
Mess = 0,
Quality = 30,
Forward = 1,
Reverse = 0,
Stitched = 0,
ReputableSupport = 1,
IsRepeat = 0,
IsSplit = 0
}, lookup[expectedMulti]);
// Multi that are far apart - allow to track individually too.
var readPairMultiFar = TestHelpers.GetPair("5M1D26M1D4M", "5M1D26M1D4M", nm: 2, nm2: 2);
IndelEvidenceHelper.FindIndelsAndRecordEvidence(readPairMultiFar.Read1, targetFinder, lookup, true, "chr1", 10);
Assert.Equal(5, lookup.Count);
// Original del shouldn't have changed
Assert.Contains(expectedDel, lookup.Keys);
ValidateEvidenceMatches(
new IndelEvidence()
{
Observations = 4,
LeftAnchor = 20,
RightAnchor = 41,
Mess = 4,
Quality = 120,
Forward = 2,
Reverse = 1,
Stitched = 1,
ReputableSupport = 3,
IsRepeat = 0,
IsSplit = 0
}, lookup[expectedDel]);
var expectedMultiFar = "chr1:104 NN>N|chr1:131 NN>N";
Assert.Contains(expectedMultiFar, lookup.Keys);
ValidateEvidenceMatches(
new IndelEvidence()
{
Observations = 1,
LeftAnchor = 5,
RightAnchor = 4,
Mess = 0,
Quality = 30,
Forward = 1,
Reverse = 0,
Stitched = 0,
ReputableSupport = 1,
IsRepeat = 0,
IsSplit = 0
}, lookup[expectedMultiFar]);
var expectedSecondSingleFromMulti = "chr1:131 NN>N";
Assert.Contains(expectedSecondSingleFromMulti, lookup.Keys);
ValidateEvidenceMatches(
new IndelEvidence()
{
Observations = 1,
LeftAnchor = 26,
RightAnchor = 4,
Mess = 1,
Quality = 30,
Forward = 1,
Reverse = 0,
Stitched = 0,
ReputableSupport = 1,
IsRepeat = 0,
IsSplit = 0
}, lookup[expectedSecondSingleFromMulti]);
}
