protected override bool ShouldSkipRead(BamAlignment alignment)
{
if (!_filterPairLowMapQ && alignment.MapQuality > 0 && alignment.MapQuality < _minMapQuality)
{
_statusCounter.AddDebugStatusCount("Skipped read below mapQ");
return(true);
}
if (alignment.IsSupplementaryAlignment())
{
_statusCounter.AddDebugStatusCount("Skipped supplementary");
return(true);
}
if (alignment.IsSecondary())
{
_statusCounter.AddDebugStatusCount("Skipped secondary");
return(true);
}
if (_filterForProperPairs && !alignment.IsProperPair())
{
_statusCounter.AddDebugStatusCount("Skipped improper pair");
return(true);
}
return(false);
}
protected override bool ShouldSkipRead(BamAlignment alignment)
{
if (!alignment.IsMapped())
{
_statusCounter.AddDebugStatusCount("Skipped not mapped");
return(true);
}
if (alignment.IsSupplementaryAlignment())
{
_statusCounter.AddDebugStatusCount("Skipped supplementary");
return(true);
}
if (_filterForProperPairs && !alignment.IsProperPair())
{
_statusCounter.AddDebugStatusCount("Skipped improper pair");
return(true);
}
if (alignment.MapQuality < _minMapQuality)
{
_statusCounter.AddDebugStatusCount("Skipped low map quality");
return(true);
}
return(false);
}
private bool ShouldSkipRead(BamAlignment alignment)
{
if (alignment.IsSupplementaryAlignment() || !alignment.IsPrimaryAlignment())
{
return(true);
}
if (_filterForProperPairs && !alignment.IsProperPair())
{
return(true);
}
return(false);
}
public void AddAlignment(BamAlignment alignment, ReadNumber readNumber = ReadNumber.NA)
{
var alignmentCopy = new BamAlignment(alignment);
if (alignment.IsPrimaryAlignment() && !alignment.IsSupplementaryAlignment())
{
if (readNumber == ReadNumber.NA)
{
if (Read1 != null && Read2 != null)
{
throw new InvalidDataException($"Already have both primary alignments for {alignment.Name}.");
}
if (Read1 == null)
{
Read1 = alignmentCopy;
}
else
{
Read2 = alignmentCopy;
}
}
else if (readNumber == ReadNumber.Read1)
{
if (Read1 != null)
{
throw new InvalidDataException($"Already have a read 1 primary alignment for {alignment.Name}.");
}
Read1 = alignmentCopy;
}
else if (readNumber == ReadNumber.Read2)
{
if (Read2 != null)
{
throw new InvalidDataException($"Already have a read 2 primary alignment for {alignment.Name}.");
}
Read2 = alignmentCopy;
}
}
else if (alignment.IsSupplementaryAlignment())
{
switch (readNumber)
{
case ReadNumber.Read1:
if (Read1SupplementaryAlignments == null)
{
Read1SupplementaryAlignments = new List <BamAlignment>();
}
Read1SupplementaryAlignments.Add(alignmentCopy);
break;
case ReadNumber.Read2:
if (Read2SupplementaryAlignments == null)
{
Read2SupplementaryAlignments = new List <BamAlignment>();
}
Read2SupplementaryAlignments.Add(alignmentCopy);
break;
case ReadNumber.NA:
if (Read1SupplementaryAlignments == null)
{
Read1SupplementaryAlignments = new List <BamAlignment>();
}
Read1SupplementaryAlignments.Add(alignmentCopy);
break;
default:
throw new ArgumentOutOfRangeException(nameof(readNumber), readNumber, null);
}
}
else
{
switch (readNumber)
{
case ReadNumber.Read1:
if (Read1SecondaryAlignments == null)
{
Read1SecondaryAlignments = new List <BamAlignment>();
}
Read1SecondaryAlignments.Add(alignmentCopy);
break;
case ReadNumber.Read2:
if (Read2SecondaryAlignments == null)
{
Read2SecondaryAlignments = new List <BamAlignment>();
}
Read2SecondaryAlignments.Add(alignmentCopy);
break;
case ReadNumber.NA:
if (Read1SecondaryAlignments == null)
{
Read1SecondaryAlignments = new List <BamAlignment>();
}
Read1SecondaryAlignments.Add(alignmentCopy);
break;
default:
throw new ArgumentOutOfRangeException(nameof(readNumber), readNumber, null);
}
}
// Set as improper once we add any alignment that is flagged as improper
if (!alignment.IsProperPair())
{
IsImproper = true;
}
}
public void AddAlignment(BamAlignment alignment, ReadNumber readNumber = ReadNumber.NA)
{
var alignmentCopy = new BamAlignment(alignment);
if (alignmentCopy.IsPrimaryAlignment() && !alignmentCopy.IsSupplementaryAlignment())
{
if (FragmentSize == 0)
{
FragmentSize = Math.Abs(alignmentCopy.FragmentLength);
// Can be either F1R2 or F2R1
NormalPairOrientation = (!alignmentCopy.IsReverseStrand() && alignmentCopy.IsMateReverseStrand()) ||
(alignmentCopy.IsReverseStrand() && !alignmentCopy.IsMateReverseStrand());
if (NormalPairOrientation)
{
if (alignmentCopy.RefID == alignmentCopy.MateRefID)
{
if (!alignmentCopy.IsReverseStrand())
{
if (alignmentCopy.Position > alignmentCopy.MatePosition)
{
// RF
NormalPairOrientation = false;
}
}
else
{
if (alignmentCopy.MatePosition > alignmentCopy.Position)
{
// RF
NormalPairOrientation = false;
}
}
}
}
}
NumPrimaryReads++;
bool useForPos = true;
if (useForPos)
{
if (alignmentCopy.Position > MaxPosition)
{
MaxPosition = alignment.Position;
}
if (alignmentCopy.Position < MinPosition)
{
MinPosition = alignment.Position;
}
}
if (readNumber == ReadNumber.NA)
{
if (Read1 != null && Read2 != null)
{
throw new InvalidDataException($"Already have both primary alignments for {alignment.Name}.");
}
if (Read1 == null)
{
Read1 = alignmentCopy;
}
else
{
Read2 = alignmentCopy;
}
}
else if (readNumber == ReadNumber.Read1)
{
if (Read1 != null)
{
throw new InvalidDataException($"Already have a read 1 primary alignment for {alignment.Name}.");
}
Read1 = alignmentCopy;
}
else if (readNumber == ReadNumber.Read2)
{
if (Read2 != null)
{
throw new InvalidDataException($"Already have a read 2 primary alignment for {alignment.Name}.");
}
Read2 = alignmentCopy;
}
}
else if (alignmentCopy.IsSupplementaryAlignment())
{
switch (readNumber)
{
case ReadNumber.Read1:
if (Read1SupplementaryAlignments == null)
{
Read1SupplementaryAlignments = new List <BamAlignment>();
}
Read1SupplementaryAlignments.Add(alignmentCopy);
break;
case ReadNumber.Read2:
if (Read2SupplementaryAlignments == null)
{
Read2SupplementaryAlignments = new List <BamAlignment>();
}
Read2SupplementaryAlignments.Add(alignmentCopy);
break;
case ReadNumber.NA:
if (Read1SupplementaryAlignments == null)
{
Read1SupplementaryAlignments = new List <BamAlignment>();
}
Read1SupplementaryAlignments.Add(alignmentCopy);
break;
default:
throw new ArgumentOutOfRangeException(nameof(readNumber), readNumber, null);
}
}
else
{
switch (readNumber)
{
case ReadNumber.Read1:
if (Read1SecondaryAlignments == null)
{
Read1SecondaryAlignments = new List <BamAlignment>();
}
Read1SecondaryAlignments.Add(alignmentCopy);
break;
case ReadNumber.Read2:
if (Read2SecondaryAlignments == null)
{
Read2SecondaryAlignments = new List <BamAlignment>();
}
Read2SecondaryAlignments.Add(alignmentCopy);
break;
case ReadNumber.NA:
if (Read1SecondaryAlignments == null)
{
Read1SecondaryAlignments = new List <BamAlignment>();
}
Read1SecondaryAlignments.Add(alignmentCopy);
break;
default:
throw new ArgumentOutOfRangeException(nameof(readNumber), readNumber, null);
}
}
// Set as improper once we add any alignment that is flagged as improper
if (!alignmentCopy.IsProperPair())
{
IsImproper = true;
}
}
