protected override bool ShouldBlacklistReadIndexer(BamAlignment alignment)
{
if (_filterPairLowMapQ)
{
if (alignment.MapQuality > 0 && alignment.MapQuality < _minMapQuality)
{
return(true);
}
}
if (_filterPairUnmapped)
{
if (!alignment.IsMapped())
{
_statusCounter.AddDebugStatusCount("Skipped not mapped");
return(true);
}
if (!alignment.IsMateMapped())
{
_statusCounter.AddDebugStatusCount("Skipped mate not mapped");
return(true);
}
}
// Only check if read is duplicate once (otherwise de novo dup finder will falsely mark dup because it has seen this read before!)
// Blacklist rather than just skipping because if one mate is duplicate, we presume the other one is too.
// Note: This breaks down is if we have a fusion read and the first mate we see is not a duplicate and the second mate is. In our case,
// (if we are not trying to mate fusions) we will flush the first mate to bam without knowing that the second mate is a dup.
// This is a highly unlikely degenerate case.
var isDuplicate = ReadIsDuplicate(alignment);
if (isDuplicate)
{
_statusCounter.AddStatusCount("Blacklisted Duplicates");
}
return(isDuplicate);
}
private static void AddReadLevelIndelMetrics(BamAlignment bamAlignment, bool isReputable, bool stitched, IndelEvidence indelMetrics,
bool isRepeat)
{
indelMetrics.Observations++;
if (stitched)
{
indelMetrics.Stitched++;
}
else
{
if (bamAlignment.IsReverseStrand())
{
indelMetrics.Reverse++;
}
else
{
indelMetrics.Forward++;
}
}
if (isReputable)
{
indelMetrics.ReputableSupport++;
}
if (isRepeat)
{
indelMetrics.IsRepeat++;
}
if (!bamAlignment.IsMateMapped() || bamAlignment.MateRefID != bamAlignment.RefID)
{
indelMetrics.IsSplit++;
}
}
private void AdjustMates(string tmpFile, BamWriter writer)
{
// Second pass: Adjust flags on mates
Logger.WriteToLog("Writing reads with corrected mate flags, {0} total remapped reads", _remappings.Count);
var read = new BamAlignment();
using (var reader = new BamReader(tmpFile))
{
while (true)
{
var result = reader.GetNextAlignment(ref read, false);
if (!result)
{
break;
}
// Adjust flags as needed:
var mateKey = string.Format("{0}-{1}", read.Name, read.IsFirstMate() ? 2 : 1);
RemapInfo info;
if (!_remappings.TryGetValue(mateKey, out info))
{
writer.WriteAlignment(read);
continue;
}
if (info.Start == -1)
{
read.SetIsMateUnmapped(true);
read.SetIsProperPair(false);
read.FragmentLength = 0;
}
else
{
read.MatePosition = info.Start;
}
if (read.IsMateMapped() && read.IsProperPair())
{
int readEnd = read.Position + (int)read.CigarData.GetReferenceSpan() - 1;
// todo jg - should FragmentLength be 0 if the reads are mapped to diff chrs
read.FragmentLength = (read.Position < info.Start
? info.End - read.Position + 1
: info.Start - readEnd - 1);
}
writer.WriteAlignment(read);
}
}
}
private bool MayOverlapMate(BamAlignment alignment)
{
if (!alignment.IsMateMapped())
{
return(false);
}
if (!alignment.IsMapped())
{
return(false);
}
if (alignment.RefID != alignment.MateRefID)
{
return(false);
}
if (Math.Abs(alignment.Position - alignment.MatePosition) > _maxPairGap)
{
return(false);
}
return(true);
}
private PairStatus SingleReadStatus(BamAlignment alignment)
{
if ((alignment.RefID != alignment.MateRefID && alignment.IsPaired()))
{
return(PairStatus.SplitChromosomes); // Stitched reads will have split ref ids too but not the same thing
}
if (((!alignment.IsMateMapped() && alignment.RefID == -1) || (!alignment.IsMapped() && alignment.MateRefID == -1)))
{
return(PairStatus.MateUnmapped);
}
if (alignment.IsDuplicate())
{
return(PairStatus.Duplicate);
}
if (_considerInsertSize)
{
if (alignment.IsPaired() && !OverlapsMate(alignment))
{
return(PairStatus.LongFragment);
}
}
return(PairStatus.Unknown);
}
protected override bool ShouldBlacklistReadIndexer(BamAlignment alignment)
{
if (_filterPairLowMapQ)
{
if (alignment.MapQuality > 0 && alignment.MapQuality < _minMapQuality)
{
return(true);
}
}
if (_filterPairUnmapped)
{
// Need to check mapped flag in addition to refid because some pairs have one mate mapped and one mate mapped right next to it but with mapq 0 and with mapping(chr: pos) information. This allows us to distinguish those from truly unmapped("don't know what the heck to do with this") reads
if (!alignment.IsMapped() && alignment.RefID == -1)
{
_statusCounter.AddDebugStatusCount("Skipped not mapped");
return(true);
}
if (!alignment.IsMateMapped() && alignment.MateRefID == -1)
{
_statusCounter.AddDebugStatusCount("Skipped mate not mapped");
return(true);
}
}
// Only check if read is duplicate once (otherwise de novo dup finder will falsely mark dup because it has seen this read before!)
// Blacklist rather than just skipping because if one mate is duplicate, we presume the other one is too.
// Note: This breaks down is if we have a fusion read and the first mate we see is not a duplicate and the second mate is. In our case,
// (if we are not trying to mate fusions) we will flush the first mate to bam without knowing that the second mate is a dup.
// This is a highly unlikely degenerate case.
var isDuplicate = ReadIsDuplicate(alignment);
if (isDuplicate)
{
_statusCounter.AddStatusCount("Blacklisted Duplicates");
}
return(isDuplicate);
}
/// <summary>
/// Bins the fragment identified by alignment. Increases bin count if the first read of a pair passes all the filters.
/// Decreases bin count if the second read of a pair does not pass all the filters.
/// </summary>
/// <param name="alignment"></param>
/// <param name="qualityThreshold">minimum mapping quality</param>
/// <param name="readNameToBinIndex">Dictionary of read name to bin index</param>
/// <param name="usableFragmentCount">number of usable fragments</param>
/// <param name="bins">predefined bins</param>
/// <param name="binIndexStart">bin index from which to start searching for the best bin</param>
public static void BinOneAlignment(BamAlignment alignment, uint qualityThreshold, Dictionary <string, int> readNameToBinIndex,
HashSet <string> samePositionReadNames, ref long usableFragmentCount, List <SampleGenomicBin> bins, ref int binIndexStart)
{
if (!alignment.IsMapped())
{
return;
}
if (!alignment.IsMateMapped())
{
return;
}
if (!alignment.IsPrimaryAlignment())
{
return;
}
if (!(alignment.IsPaired() && alignment.IsProperPair()))
{
return;
}
bool duplicateFailedQCLowQuality = IsDuplicateFailedQCLowQuality(alignment, qualityThreshold);
// Check whether we have binned the fragment using the mate
if (readNameToBinIndex.ContainsKey(alignment.Name))
{
// Undo binning when one of the reads is a duplicate, fails QC or has low mapping quality
if (duplicateFailedQCLowQuality)
{
usableFragmentCount--;
bins[readNameToBinIndex[alignment.Name]].Count--;
}
readNameToBinIndex.Remove(alignment.Name); // clean up
return;
}
if (duplicateFailedQCLowQuality)
{
return;
}
if (alignment.RefID != alignment.MateRefID)
{
return;
} // does this ever happen?
if (IsRightMostInPair(alignment))
{
return;
} // look at only one read of the pair
// handle the case where alignment.Position == alignment.MatePosition
if (alignment.Position == alignment.MatePosition)
{
if (samePositionReadNames.Contains(alignment.Name))
{
samePositionReadNames.Remove(alignment.Name);
return;
}
samePositionReadNames.Add(alignment.Name);
}
if (alignment.FragmentLength == 0)
{
return;
} // Janus-SRS-190: 0 when the information is unavailable
// Try to bin the fragment
int fragmentStart = alignment.Position; // 0-based, inclusive
int fragmentStop = alignment.Position + alignment.FragmentLength; // 0-based, exclusive
while (binIndexStart < bins.Count && bins[binIndexStart].Stop <= fragmentStart) // Bins[binIndexStart] on the left of the fragment
{
binIndexStart++;
}
if (binIndexStart >= bins.Count)
{
return;
} // all the remaining fragments are on the right of the last bin
// now Bins[binIndexStart].Stop > fragmentStart
int bestBinIndex = FindBestBin(bins, binIndexStart, fragmentStart, fragmentStop);
if (bestBinIndex >= 0) // Bin the fragment
{
usableFragmentCount++;
bins[bestBinIndex].Count++;
readNameToBinIndex[alignment.Name] = bestBinIndex;
}
}
/// <summary>
/// Bins the fragment identified by alignment. Increases bin count if the first read of a pair passes all the filters.
/// Decreases bin count if the second read of a pair does not pass all the filters.
/// </summary>
/// <param name="alignment"></param>
/// <param name="qualityThreshold">minimum mapping quality</param>
/// <param name="readNameToBinIndex">Dictionary of read name to bin index</param>
/// <param name="usableFragmentCount">number of usable fragments</param>
/// <param name="bins">predefined bins</param>
/// <param name="binIndexStart">bin index from which to start searching for the best bin</param>
public static void BinOneAlignment(BamAlignment alignment, uint qualityThreshold, Dictionary<string, int> readNameToBinIndex,
HashSet<string> samePositionReadNames, ref long usableFragmentCount, List<GenomicBin> bins, ref int binIndexStart)
{
if (!alignment.IsMapped()) { return; }
if (!alignment.IsMateMapped()) { return; }
if (!alignment.IsPrimaryAlignment()) { return; }
if (!(alignment.IsPaired() && alignment.IsProperPair())) { return; }
bool duplicateFailedQCLowQuality = IsDuplicateFailedQCLowQuality(alignment, qualityThreshold);
// Check whether we have binned the fragment using the mate
if (readNameToBinIndex.ContainsKey(alignment.Name))
{
// Undo binning when one of the reads is a duplicate, fails QC or has low mapping quality
if (duplicateFailedQCLowQuality)
{
usableFragmentCount--;
bins[readNameToBinIndex[alignment.Name]].Count--;
}
readNameToBinIndex.Remove(alignment.Name); // clean up
return;
}
if (duplicateFailedQCLowQuality) { return; }
if (alignment.RefID != alignment.MateRefID) { return; } // does this ever happen?
if (IsRightMostInPair(alignment)) { return; } // look at only one read of the pair
// handle the case where alignment.Position == alignment.MatePosition
if (alignment.Position == alignment.MatePosition)
{
if (samePositionReadNames.Contains(alignment.Name))
{
samePositionReadNames.Remove(alignment.Name);
return;
}
samePositionReadNames.Add(alignment.Name);
}
if (alignment.FragmentLength == 0) { return; } // Janus-SRS-190: 0 when the information is unavailable
// Try to bin the fragment
int fragmentStart = alignment.Position; // 0-based, inclusive
int fragmentStop = alignment.Position + alignment.FragmentLength; // 0-based, exclusive
while (binIndexStart < bins.Count && bins[binIndexStart].Stop <= fragmentStart) // Bins[binIndexStart] on the left of the fragment
{
binIndexStart++;
}
if (binIndexStart >= bins.Count) { return; } // all the remaining fragments are on the right of the last bin
// now Bins[binIndexStart].Stop > fragmentStart
int bestBinIndex = FindBestBin(bins, binIndexStart, fragmentStart, fragmentStop);
if (bestBinIndex >= 0) // Bin the fragment
{
usableFragmentCount++;
bins[bestBinIndex].Count++;
readNameToBinIndex[alignment.Name] = bestBinIndex;
}
}
