public void IsDuplicate()
{
var duplicateIdentifier = new AlignmentFlagDuplicateIdentifier();
var alignment = new BamAlignment();
alignment.SetIsDuplicate(true);
Assert.True(duplicateIdentifier.IsDuplicate(alignment));
alignment.SetIsDuplicate(false);
Assert.False(duplicateIdentifier.IsDuplicate(alignment));
}
public void Reset()
{
var alignment = new BamAlignment
{
Bases = "ACTC",
Position = 5,
MapQuality = 343,
MatePosition = 12312,
Qualities = new[] { (byte)20, (byte)21, (byte)30, (byte)40 },
CigarData = new CigarAlignment("1S3M")
};
alignment.SetIsUnmapped(false);
alignment.SetIsSecondaryAlignment(false);
alignment.SetIsDuplicate(true);
alignment.SetIsProperPair(true);
var read = new Read("chr1", alignment);
read.StitchedCigar = new CigarAlignment("7M");
read.SequencedBaseDirectionMap = new[] { DirectionType.Forward, DirectionType.Reverse, DirectionType.Stitched, DirectionType.Reverse };
alignment.SetIsDuplicate(false);
alignment.MatePosition = 555;
read.Reset("chr2", alignment);
Assert.Equal(556, read.MatePosition);
Assert.False(read.IsPcrDuplicate);
Assert.Equal("chr2", read.Chromosome);
var stitchedCigar = "1S3M1S";
alignment.TagData = DomainTestHelper.GetXCTagData(stitchedCigar);
read.Reset("chr3", alignment);
Assert.Equal(556, read.MatePosition);
Assert.False(read.IsPcrDuplicate);
Assert.Equal("chr3", read.Chromosome);
Assert.Equal(stitchedCigar, read.StitchedCigar.ToString());
}
private Read CreateRead(string chr, string sequence, int position, string name, bool isMapped = true,
bool isPrimaryAlignment = true, bool isProperPair = true, bool isDuplicate = false, int mapQuality = 10, bool addCigarData = true)
{
var alignment = new BamAlignment()
{
Bases = sequence, Position = position, Name = name, MapQuality = (uint)mapQuality
};
alignment.SetIsUnmapped(!isMapped);
alignment.SetIsSecondaryAlignment(!isPrimaryAlignment);
alignment.SetIsDuplicate(isDuplicate);
alignment.SetIsProperPair(isProperPair);
if (addCigarData)
{
alignment.CigarData = new CigarAlignment(sequence.Length + "M");
}
return(new Read(chr, alignment));
}
public void FromBam()
{
var alignment = new BamAlignment
{
Bases = "ATCTTA",
Position = 100,
MatePosition = 500,
Name = "test",
CigarData = new CigarAlignment("5M1S"),
MapQuality = 10,
Qualities = new[] { (byte)10, (byte)20, (byte)30 }
};
alignment.SetIsDuplicate(true);
alignment.SetIsProperPair(true);
alignment.SetIsSecondaryAlignment(true);
alignment.SetIsUnmapped(true);
var read = new Read("chr1", alignment);
Assert.Equal(read.Chromosome, "chr1");
Assert.Equal(read.Sequence, alignment.Bases);
Assert.Equal(read.Position, alignment.Position + 1);
Assert.Equal(read.MatePosition, alignment.MatePosition + 1);
Assert.Equal(read.Name, alignment.Name);
Assert.Equal(read.CigarData, alignment.CigarData);
Assert.Equal(read.IsMapped, alignment.IsMapped());
Assert.Equal(read.IsProperPair, alignment.IsProperPair());
Assert.Equal(read.IsPrimaryAlignment, alignment.IsPrimaryAlignment());
Assert.Equal(read.IsPcrDuplicate, alignment.IsDuplicate());
foreach (var direction in read.SequencedBaseDirectionMap)
{
Assert.Equal(direction, DirectionType.Forward);
}
for (var i = 0; i < read.Qualities.Length; i++)
{
Assert.Equal(read.Qualities[i], alignment.Qualities[i]);
}
}
public void DeepCopy()
{
var alignment = new BamAlignment
{
Bases = "ACTC",
Position = 5,
MapQuality = 343,
MatePosition = 12312,
Qualities = new[] { (byte)20, (byte)21, (byte)30, (byte)40 },
CigarData = new CigarAlignment("1S3M")
};
alignment.SetIsUnmapped(false);
alignment.SetIsSecondaryAlignment(false);
alignment.SetIsDuplicate(true);
alignment.SetIsProperPair(true);
var read = new Read("chr1", alignment);
read.StitchedCigar = new CigarAlignment("7M");
read.SequencedBaseDirectionMap = new[] { DirectionType.Forward, DirectionType.Reverse, DirectionType.Stitched, DirectionType.Reverse };
var clonedRead = read.DeepCopy();
DomainTestHelper.CompareReads(read, clonedRead);
// verify the arrays are deep copies
read.PositionMap[0] = 1000;
Assert.False(clonedRead.PositionMap[0] == 1000);
read.SequencedBaseDirectionMap[0] = DirectionType.Stitched;
Assert.False(clonedRead.SequencedBaseDirectionMap[0] == DirectionType.Stitched);
read.Qualities[0] = 11;
Assert.False(clonedRead.Qualities[0] == 11);
read.CigarData.Reverse();
Assert.False(((Read)clonedRead).CigarData.ToString() == read.CigarData.ToString());
}
public void BamAlignmentFlag_Setter_Tests()
{
var alignment = new BamAlignment();
//Set Failed QC
alignment.SetIsFailedQC(true);
Assert.Equal((uint)512, alignment.AlignmentFlag);
alignment.SetIsFailedQC(false);
Assert.Equal((uint)0, alignment.AlignmentFlag);
//Set Mate Unmapped
alignment.SetIsMateUnmapped(true);
Assert.Equal((uint)8, alignment.AlignmentFlag);
alignment.SetIsMateUnmapped(false);
Assert.Equal((uint)0, alignment.AlignmentFlag);
//Set Mate Reverse Strand
alignment.SetIsMateReverseStrand(true);
Assert.Equal((uint)32, alignment.AlignmentFlag);
alignment.SetIsMateReverseStrand(false);
Assert.Equal((uint)0, alignment.AlignmentFlag);
//Set Is Paired
alignment.SetIsPaired(true);
Assert.Equal((uint)1, alignment.AlignmentFlag);
alignment.SetIsPaired(false);
Assert.Equal((uint)0, alignment.AlignmentFlag);
//Set Duplicate
alignment.SetIsDuplicate(true);
Assert.Equal((uint)1024, alignment.AlignmentFlag);
alignment.SetIsDuplicate(false);
Assert.Equal((uint)0, alignment.AlignmentFlag);
//Set First Mate
alignment.SetIsFirstMate(true);
Assert.Equal((uint)64, alignment.AlignmentFlag);
alignment.SetIsFirstMate(false);
Assert.Equal((uint)0, alignment.AlignmentFlag);
//Set Proper Pair
alignment.SetIsProperPair(true);
Assert.Equal((uint)2, alignment.AlignmentFlag);
alignment.SetIsProperPair(false);
Assert.Equal((uint)0, alignment.AlignmentFlag);
//Set Reverse Strand
alignment.SetIsReverseStrand(true);
Assert.Equal((uint)16, alignment.AlignmentFlag);
alignment.SetIsReverseStrand(false);
Assert.Equal((uint)0, alignment.AlignmentFlag);
//Set Secondary Alignment
alignment.SetIsSecondaryAlignment(true);
Assert.Equal((uint)256, alignment.AlignmentFlag);
alignment.SetIsSecondaryAlignment(false);
Assert.Equal((uint)0, alignment.AlignmentFlag);
//Set Second Mate
alignment.SetIsSecondMate(true);
Assert.Equal((uint)128, alignment.AlignmentFlag);
alignment.SetIsSecondMate(false);
Assert.Equal((uint)0, alignment.AlignmentFlag);
//Set Unmapped
alignment.SetIsUnmapped(true);
Assert.Equal((uint)4, alignment.AlignmentFlag);
alignment.SetIsUnmapped(false);
Assert.Equal((uint)0, alignment.AlignmentFlag);
}