public static BamAlignment StitchifyBamAlignment(ReadPair pair, Read read, char read1dir, char read2dir)
{
var alignment = new BamAlignment(read.BamAlignment);
alignment.SetIsFirstMate(false);
alignment.SetIsProperPair(false);
var tagUtils = new TagUtils();
if (read.StitchedCigar != null)
{
alignment.CigarData = read.StitchedCigar;
}
if (read.CigarDirections != null)
{
tagUtils.AddStringTag("XD", read.CigarDirections.ToString());
}
// if the original reads had UMIs and were collapsed, they will have XU(Z), XV(i), XW(i)
// these need to be copied to correctly populate some fields in the called variants
if (pair.Read1.TagData != null && pair.Read1.TagData.Length > 0)
{
var xu = pair.Read1.GetStringTag("XU");
if (xu != null)
{
tagUtils.AddStringTag("XU", xu);
}
var xv = pair.Read1.GetIntTag("XV");
if (xv.HasValue)
{
tagUtils.AddIntTag("XV", xv.Value);
}
var xw = pair.Read1.GetIntTag("XW");
if (xw.HasValue)
{
tagUtils.AddIntTag("XW", xw.Value);
}
}
var xr = string.Format("{0}{1}", read1dir, read2dir);
tagUtils.AddStringTag("XR", xr);
var tagData = tagUtils.ToBytes();
var existingTags = alignment.TagData;
if (existingTags == null)
{
alignment.TagData = tagData;
}
else
{
alignment.AppendTagData(tagData);
}
return(alignment);
}
public static byte[] GetReadCountsTagData(int?xw, int?xv)
{
var tagUtils = new TagUtils();
if (xw.HasValue)
{
tagUtils.AddIntTag("XW", xw.Value);
}
if (xv.HasValue)
{
tagUtils.AddIntTag("XV", xv.Value);
}
return(tagUtils.ToBytes());
}
public static byte[] GetReadCountsTagData(int?x1, int?x2)
{
var tagUtils = new TagUtils();
if (x1.HasValue)
{
tagUtils.AddIntTag("X1", x1.Value);
}
if (x2.HasValue)
{
tagUtils.AddIntTag("X2", x2.Value);
}
return(tagUtils.ToBytes());
}
private BamAlignment CreateAlignment(string name, int position, string cigar, string bases, int nm = -1, uint mapq = 1)
{
var alignment = new BamAlignment();
alignment.Name = name;
alignment.Position = position;
alignment.RefID = 1;
alignment.MapQuality = mapq;
alignment.CigarData = new CigarAlignment(cigar);
alignment.Bases = bases;
alignment.Qualities = new byte[alignment.Bases.Length];
alignment.Qualities = Enumerable.Repeat((byte)30, alignment.Bases.Length).ToArray(); // Generates quality scores of 30
alignment.SetIsProperPair(true);
var tagUtils = new TagUtils();
if (nm >= 0)
{
tagUtils.AddIntTag("NM", nm);
}
alignment.TagData = tagUtils.ToBytes();
return(alignment);
}
public void GetTag_Tests()
{
// create a tag
TagUtils tagUtils = new TagUtils();
tagUtils.AddIntTag("NM", 5);
tagUtils.AddStringTag("XU", "ABCD");
tagUtils.AddCharTag("XP", '?');
byte[] tagData = tagUtils.ToBytes();
var alignment = new BamAlignment()
{
TagData = tagData
};
// string tag scenarios
Assert.Equal("ABCD", alignment.GetStringTag("XU"));
Assert.Equal("?", alignment.GetStringTag("XP"));
Assert.Throws <ApplicationException>(() => alignment.GetStringTag("NM"));
Assert.Equal(null, alignment.GetStringTag("AB"));
}
public static ReadPair GetPair(string cigar1, string cigar2, uint mapq1 = 30, uint mapq2 = 30, PairStatus pairStatus = PairStatus.Paired, bool singleReadOnly = false, int nm = 0, int read2Offset = 0, int?nm2 = null, string name = null, string basesRaw = "AAAGTTTTCCCCCCCCCCCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", int read1Position = 99, string read1Bases = null, string read2Bases = null)
{
int nmRead2 = nm2 ?? nm;
var tagUtils = new TagUtils();
if (nm >= 0)
{
tagUtils.AddIntTag("NM", nm);
}
var cigarAln1 = new CigarAlignment(cigar1);
var qualities1 = new List <byte>();
for (int i = 0; i < cigarAln1.GetReadSpan(); i++)
{
qualities1.Add(30);
}
//var basesRaw = "AAAGTTTTCCCCCCCCCCCC";
var alignment = new BamAlignment
{
Name = name ?? "hi:1:2:3:4:5:6",
RefID = 1,
Position = read1Position,
Bases = read1Bases ?? basesRaw.Substring(0, (int)cigarAln1.GetReadSpan()),
CigarData = cigarAln1,
Qualities = qualities1.ToArray(),
MapQuality = mapq1
};
alignment.TagData = tagUtils.ToBytes();
if (!singleReadOnly)
{
alignment.SetIsProperPair(true);
alignment.MateRefID = 1;
}
var pair = new ReadPair(alignment);
if (!singleReadOnly)
{
alignment.SetIsMateUnmapped(false);
var tagUtils2 = new TagUtils();
if (nmRead2 >= 0)
{
tagUtils2.AddIntTag("NM", nmRead2);
}
var cigarAln2 = new CigarAlignment(cigar2);
var qualities2 = new List <byte>();
for (int i = 0; i < cigarAln2.GetReadSpan(); i++)
{
qualities2.Add(30);
}
var alignment2 = new BamAlignment
{
Name = "hi:1:2:3:4:5:6",
RefID = 1,
Position = read1Position + read2Offset,
Bases = read2Bases ?? basesRaw.Substring(read2Offset, (int)cigarAln2.GetReadSpan()),
CigarData = cigarAln2,
Qualities = qualities2.ToArray(),
MapQuality = mapq2
};
alignment2.MateRefID = pair.Read1.RefID;
alignment2.SetIsProperPair(true);
alignment2.SetIsSecondMate(true);
alignment2.SetIsReverseStrand(true);
alignment2.TagData = tagUtils2.ToBytes();
pair.AddAlignment(alignment2);
}
pair.PairStatus = pairStatus;
return(pair);
}
private void ExtractReads(bool addUmiTags)
{
var refIdMapping = new Dictionary <int, string>()
{
{ 1, "chr1" }
};
var stitcher = StitcherTestHelpers.GetStitcher(10, false);
var readStatusCounter = new ReadStatusCounter();
var pairHandler = new PairHandler(refIdMapping, stitcher, readStatusCounter, filterUnstitchablePairs: true);
var alignment1 = new BamAlignment()
{
AlignmentFlag = 0,
Bases = "ABCF",
Bin = 4,
CigarData = new CigarAlignment("2S2M"),
FragmentLength = 42,
MapQuality = 30,
MatePosition = 2,
MateRefID = 43,
Name = "Read1",
Position = 1,
Qualities = new byte[4],
RefID = 1,
TagData = new byte[0]
};
var tagUtils = new TagUtils();
tagUtils.AddStringTag("BC", "14");
tagUtils.AddIntTag("SM", 40);
if (addUmiTags)
{
tagUtils.AddIntTag("XV", 1);
tagUtils.AddIntTag("XW", 2);
tagUtils.AddStringTag("XU", "ABBA-ZABBA");
}
alignment1.AppendTagData(tagUtils.ToBytes());
var alignment2 = new BamAlignment()
{
AlignmentFlag = 0,
Bases = "ABCF",
Bin = 4,
CigarData = new CigarAlignment("2S2M"),
FragmentLength = 42,
MapQuality = 30,
MatePosition = 2,
MateRefID = 43,
Name = "Read1",
Position = 1,
Qualities = new byte[4],
RefID = 1,
TagData = new byte[0]
};
var tagUtils2 = new TagUtils();
tagUtils2.AddIntTag("NM", 5);
tagUtils2.AddStringTag("BC", "14");
tagUtils2.AddIntTag("SM", 20);
if (addUmiTags)
{
tagUtils2.AddIntTag("XV", 1);
tagUtils2.AddIntTag("XW", 2);
tagUtils2.AddStringTag("XU", "ABBA-ZABBA");
}
alignment2.AppendTagData(tagUtils2.ToBytes());
var readPair = new ReadPair(alignment1);
readPair.AddAlignment(alignment2);
var alignmentResults = pairHandler.ExtractReads(readPair);
Assert.Equal(1, alignmentResults.Count);
var alignment = alignmentResults[0];
Assert.NotNull(alignment.GetStringTag("XD"));
Assert.Null(alignment.GetIntTag("NM"));
Assert.Null(alignment.GetStringTag("BC"));
Assert.Null(alignment.GetIntTag("SM"));
if (addUmiTags)
{
Assert.Equal("ABBA-ZABBA", alignment.GetStringTag("XU"));
Assert.Equal(1, alignment.GetIntTag("XV"));
Assert.Equal(2, alignment.GetIntTag("XW"));
}
}