public void AddAndGetCollapsedCount_AlleleN(ReadCollapsedType type)
{
int minQuality = 20;
var stateManager = new CollapsedRegionStateManager(false, minQuality);
var readpair = ReadTestHelper.CreateProperReadPair("test", 6, type, pos: 10,
matePos: 15, minBaseQuality: 30, candidateBases: "N"); // Generate read pairs only contain "N"
stateManager.AddAlleleCounts(readpair.Item1);
stateManager.AddAlleleCounts(readpair.Item2);
Assert.Equal(0, stateManager.GetCollapsedReadCount(10, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(11, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(12, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(13, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(14, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(15, type)); // overlapping
Assert.Equal(0, stateManager.GetCollapsedReadCount(16, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(17, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(18, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(19, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(20, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(9, type));
}
public void AddAndGetCollapsedCount_minQuality(ReadCollapsedType type)
{
int minQuality = 35;
var stateManager = new CollapsedRegionStateManager(false, minQuality);
var readpair = ReadTestHelper.CreateProperReadPair("test", 6, type, pos: 10, matePos: 15, minBaseQuality: 30);
// all base quality less than min quality, no count
stateManager.AddAlleleCounts(readpair.Item1);
stateManager.AddAlleleCounts(readpair.Item2);
Assert.Equal(0, stateManager.GetCollapsedReadCount(10, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(11, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(12, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(13, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(14, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(15, type)); // overlapping
Assert.Equal(0, stateManager.GetCollapsedReadCount(16, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(17, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(18, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(19, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(20, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(9, type));
}
public void AddAndGetCollapsedCount_NonCollapsedBAM(ReadCollapsedType type)
{
int minQuality = 20;
// non collapsed BAM (no reco @PG line in BAM header)
var stateManager = new RegionStateManager(false, minQuality, expectStitchedReads: true);
var readpair = ReadTestHelper.CreateProperReadPair("test", 6, type, pos: 10, matePos: 15);
stateManager.AddAlleleCounts(readpair.Item1);
stateManager.AddAlleleCounts(readpair.Item2);
Assert.Equal(0, stateManager.GetCollapsedReadCount(10, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(11, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(12, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(13, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(14, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(15, type)); // overlapping
Assert.Equal(0, stateManager.GetCollapsedReadCount(16, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(17, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(18, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(19, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(20, type));
Assert.Equal(0, stateManager.GetCollapsedReadCount(9, type));
}
public virtual int GetCollapsedReadCount(int position, ReadCollapsedType directionType)
{
return(0); // default behavior for non-collapsed and/or non-stitched BAM
}
public override int GetCollapsedReadCount(int position, ReadCollapsedType directionType)
{
var region = GetBlock(position, false) as CollapsedRegionState;
return(region == null ? 0 : region.GetCollapsedReadCount(position, directionType));
}
public static Tuple <Read, Read> CreateProperReadPair(string nameBase, int sequencelength, ReadCollapsedType type,
string chrName = "chr1", int pos = 10, int matePos = 100, byte minBaseQuality = 30, string candidateBases = "ACGT")
{
Read read1 = null;
Read read2 = null;
switch (type)
{
case ReadCollapsedType.SimplexForwardStitched:
read1 = CreateRead(chrName, RandomBases(sequencelength, candidateBases), pos, matePosition: matePos, qualityForAll: minBaseQuality);
read2 = CreateRead(chrName, RandomBases(sequencelength, candidateBases), matePos, matePosition: pos, isReverseMapped: true, qualityForAll: minBaseQuality);
read1.BamAlignment.TagData = GetXDXRTagData($"{sequencelength}S", "FR");
read1.BamAlignment.AppendTagData(GetReadCountsTagData(null, 10));
read2.BamAlignment.TagData = GetXDXRTagData($"{sequencelength}S", "FR");
read2.BamAlignment.AppendTagData(GetReadCountsTagData(null, 10));
break;
case ReadCollapsedType.SimplexForwardNonStitched:
read1 = CreateRead(chrName, RandomBases(sequencelength, candidateBases), pos, matePosition: matePos, qualityForAll: minBaseQuality);
read2 = CreateRead(chrName, RandomBases(sequencelength, candidateBases), matePos, matePosition: pos, isReverseMapped: true, qualityForAll: minBaseQuality);
read1.BamAlignment.TagData = GetXDXRTagData($"{null}", "FR");
read1.BamAlignment.AppendTagData(GetReadCountsTagData(null, 10));
read2.BamAlignment.TagData = GetXDXRTagData($"{null}", "FR");
read2.BamAlignment.AppendTagData(GetReadCountsTagData(null, 10));
break;
case ReadCollapsedType.SimplexReverseStitched:
read1 = CreateRead(chrName, RandomBases(sequencelength, candidateBases), matePos, matePosition: pos, isReverseMapped: true, qualityForAll: minBaseQuality);
read2 = CreateRead(chrName, RandomBases(sequencelength, candidateBases), pos, matePosition: matePos, qualityForAll: minBaseQuality);
read1.BamAlignment.TagData = GetXDXRTagData($"{sequencelength}S", "RF");
read1.BamAlignment.AppendTagData(GetReadCountsTagData(null, 10));
read2.BamAlignment.TagData = GetXDXRTagData($"{sequencelength}S", "RF");
read2.BamAlignment.AppendTagData(GetReadCountsTagData(null, 10));
break;
case ReadCollapsedType.SimplexReverseNonStitched:
read1 = CreateRead(chrName, RandomBases(sequencelength, candidateBases), matePos, matePosition: pos, isReverseMapped: true, qualityForAll: minBaseQuality);
read2 = CreateRead(chrName, RandomBases(sequencelength, candidateBases), pos, matePosition: matePos, qualityForAll: minBaseQuality);
read1.BamAlignment.TagData = GetReadCountsTagData(null, 10);
read1.BamAlignment.AppendTagData(GetXDXRTagData($"{null}", "RF"));
read2.BamAlignment.TagData = GetReadCountsTagData(null, 10);
read2.BamAlignment.AppendTagData(GetXDXRTagData($"{null}", "RF"));
break;
case ReadCollapsedType.DuplexStitched:
read1 = CreateRead(chrName, RandomBases(sequencelength, candidateBases), pos, matePosition: matePos, qualityForAll: minBaseQuality);
read2 = CreateRead(chrName, RandomBases(sequencelength, candidateBases), matePos, matePosition: pos, qualityForAll: minBaseQuality);
read1.BamAlignment.TagData = GetXDXRTagData($"{sequencelength}S", "RF");
read1.BamAlignment.AppendTagData(GetReadCountsTagData(1, 10));
read2.BamAlignment.TagData = GetXDXRTagData($"{sequencelength}S", "RF");
read2.BamAlignment.AppendTagData(GetReadCountsTagData(1, 10));
break;
case ReadCollapsedType.DuplexNonStitched:
read1 = CreateRead(chrName, RandomBases(sequencelength, candidateBases), pos, matePosition: matePos, qualityForAll: minBaseQuality);
read2 = CreateRead(chrName, RandomBases(sequencelength, candidateBases), matePos, matePosition: pos, qualityForAll: minBaseQuality);
read1.BamAlignment.TagData = GetReadCountsTagData(1, 10);
read2.BamAlignment.TagData = GetReadCountsTagData(1, 10);
break;
default:
throw new Exception("unknown type");
}
Assert.NotNull(read1);
Assert.NotNull(read2);
read1.BamAlignment.SetIsProperPair(true);
read2.BamAlignment.SetIsProperPair(true);
read1.BamAlignment.SetIsFirstMate(true);
read1.BamAlignment.SetIsSecondMate(false);
read2.BamAlignment.SetIsSecondMate(true);
read2.BamAlignment.SetIsFirstMate(false);
if (read1.Chromosome == read2.Chromosome)
{
// might not be same as pisces defintion
read1.BamAlignment.FragmentLength =
Math.Abs(read1.Position - read2.Position);
read2.BamAlignment.FragmentLength =
Math.Abs(read1.Position - read2.Position);
}
else
{
// FragmentLength be 0 if the reads are mapped to diff chrs
read1.BamAlignment.FragmentLength = 0;
read2.BamAlignment.FragmentLength = 0;
}
return(new Tuple <Read, Read>(read1, read2));
}
