public static BamAlignment CreateBamAlignment(string sequence, int position,
int matePosition, byte qualityForAll, bool isReverseMapped, uint mapQ = 30, byte[] qualities = null, CigarAlignment cigar = null, string name = null, bool isFirstMate = true)
{
var bamAlignment = new BamAlignment
{
Bases = sequence,
Position = position - 1,
CigarData = cigar ?? new CigarAlignment(sequence.Length + "M"),
Qualities = qualities ?? Enumerable.Repeat(qualityForAll, sequence.Length).ToArray(),
MatePosition = matePosition - 1,
TagData = new byte[0],
RefID = 1,
MateRefID = 1,
Name = name ?? "Alignment"
};
bamAlignment.SetIsFirstMate(isFirstMate);
bamAlignment.MapQuality = mapQ;
bamAlignment.SetIsReverseStrand(isReverseMapped);
bamAlignment.SetIsMateReverseStrand(!isReverseMapped);
return(bamAlignment);
}
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);
}
