public void GetClippedCigar()
{
// from middle
Assert.Equal("3M", CigarExtensions.GetClippedCigar(new CigarAlignment("3S6M"), 3, 6).ToString());
Assert.Equal("3M", CigarExtensions.GetClippedCigar(new CigarAlignment("3S3D6M"), 3, 6, false).ToString());
Assert.Equal("3M", CigarExtensions.GetClippedCigar(new CigarAlignment("3S3M3D4M"), 3, 6, false).ToString());
Assert.Equal("3M3D", CigarExtensions.GetClippedCigar(new CigarAlignment("3S3M3D4M"), 3, 6).ToString());
Assert.Equal("3D3M", CigarExtensions.GetClippedCigar(new CigarAlignment("3S3D4M"), 3, 6).ToString());
Assert.Equal("3D3M", CigarExtensions.GetClippedCigar(new CigarAlignment("1S1D2S3D4M"), 3, 6).ToString());
// readcycles < 0
Assert.Equal("", CigarExtensions.GetClippedCigar(new CigarAlignment("5M3D7M"), 0, 0).ToString());
Assert.Equal("", CigarExtensions.GetClippedCigar(new CigarAlignment("5M3D7M"), 0, 0).ToString());
Assert.Equal("", CigarExtensions.GetClippedCigar(new CigarAlignment("5M3D7M"), -1, -1).ToString());
//readcycles > 0
Assert.Equal("1M", CigarExtensions.GetClippedCigar(new CigarAlignment("5M3D7M"), 0, 1).ToString());
Assert.Equal("5M3D2M", CigarExtensions.GetClippedCigar(new CigarAlignment("5M3D7M"), 0, 7).ToString());
Assert.Equal("5M3D", CigarExtensions.GetClippedCigar(new CigarAlignment("5M3D7M"), 0, 5).ToString());
// skip end dels if specified (but not internal dels)
Assert.Equal("5M3D2M", CigarExtensions.GetClippedCigar(new CigarAlignment("5M3D7M"), 0, 7, false).ToString());
Assert.Equal("5M", CigarExtensions.GetClippedCigar(new CigarAlignment("5M3D7M"), 0, 5, false).ToString());
//softclips
Assert.Equal("2M1S", CigarExtensions.GetClippedCigar(new CigarAlignment("2M1S"), 0, 3).ToString());
Assert.Equal("2M", CigarExtensions.GetClippedCigar(new CigarAlignment("2M1S"), 0, 2).ToString());
}
public void HasOperationAtOpIndex()
{
var alignment = new CigarAlignment("5M3D4M7I2S8M");
Assert.True(alignment.HasOperationAtOpIndex(3, 'I'));
Assert.False(alignment.HasOperationAtOpIndex(5, 'D'));
Assert.False(CigarExtensions.HasOperationAtOpIndex(null, 3, 'D'));
Assert.False(CigarExtensions.HasOperationAtOpIndex(null, 3, 'D', true));
Assert.True(alignment.HasOperationAtOpIndex(1, 'S', true));
Assert.False(alignment.HasOperationAtOpIndex(2, 'D', true));
Assert.False(alignment.HasOperationAtOpIndex(-1, 'D', true));
Assert.False(alignment.HasOperationAtOpIndex(8, 'D', true));
}
public void SetOpsForRead(ReadNumber num, List <StitchableItem> ops)
{
if (num == ReadNumber.Read1)
{
R1Ops = ops;
R1OpsCount = ops.Count;
R1HasReferenceSpan = ops.Any(x => CigarExtensions.IsReferenceSpan(x.CigarOp));
}
else
{
R2Ops = ops;
R2OpsCount = ops.Count;
R2HasReferenceSpan = ops.Any(x => CigarExtensions.IsReferenceSpan(x.CigarOp));
}
}
public void AddOpsForRead(ReadNumber num, List <StitchableItem> ops)
{
if (num == ReadNumber.Read1)
{
R1OpsCount += ops.Count;
R1Ops.AddRange(ops);
if (!R1HasReferenceSpan)
{
R1HasReferenceSpan = ops.Any(x => CigarExtensions.IsReferenceSpan(x.CigarOp));
}
}
else
{
R2OpsCount += ops.Count;
R2Ops.AddRange(ops);
if (!R2HasReferenceSpan)
{
R2HasReferenceSpan = ops.Any(x => CigarExtensions.IsReferenceSpan(x.CigarOp));
}
}
}
public void AddOpsForRead(ReadNumber num, StitchableItem ops)
{
if (num == ReadNumber.Read1)
{
R1OpsCount++;
R1Ops.Add(ops);
if (CigarExtensions.IsReferenceSpan(ops.CigarOp))
{
R1HasReferenceSpan = true;
}
}
else
{
R2OpsCount++;
R2Ops.Add(ops);
if (CigarExtensions.IsReferenceSpan(ops.CigarOp))
{
R2HasReferenceSpan = true;
}
}
}
public void GetTrimmed()
{
//readcycles < 0
Assert.Equal("", CigarExtensions.GetTrimmed(new CigarAlignment("5M3D7M"), 0).ToString());
Assert.Equal("", CigarExtensions.GetTrimmed(new CigarAlignment("5M3D7M"), 0, true).ToString());
Assert.Equal("", CigarExtensions.GetTrimmed(new CigarAlignment("5M3D7M"), -1, true).ToString());
//readcycles > 0
Assert.Equal("1M", CigarExtensions.GetTrimmed(new CigarAlignment("5M3D7M"), 1).ToString());
Assert.Equal("1M", CigarExtensions.GetTrimmed(new CigarAlignment("5M3D7M"), 1, true).ToString());
Assert.Equal("5M3D2M", CigarExtensions.GetTrimmed(new CigarAlignment("5M3D7M"), 7).ToString());
Assert.Equal("3D7M", CigarExtensions.GetTrimmed(new CigarAlignment("5M3D7M"), 7, true).ToString());
Assert.Equal("5M3D", CigarExtensions.GetTrimmed(new CigarAlignment("5M3D7M"), 5).ToString());
// skip end dels if specified (but not internal dels)
Assert.Equal("7M", CigarExtensions.GetTrimmed(new CigarAlignment("5M3D7M"), 7, true, false).ToString());
Assert.Equal("7M", CigarExtensions.GetTrimmed(new CigarAlignment("4M1D1M3D7M"), 7, true, false).ToString());
Assert.Equal("4M1D3M", CigarExtensions.GetTrimmed(new CigarAlignment("5M3D4M1D3M"), 7, true, false).ToString());
Assert.Equal("5M3D2M", CigarExtensions.GetTrimmed(new CigarAlignment("5M3D7M"), 7, false, false).ToString());
Assert.Equal("5M", CigarExtensions.GetTrimmed(new CigarAlignment("5M3D7M"), 5, false, false).ToString());
}
