public void GetBetterResult()
{
var comparer = new BasicAlignmentComparer();
var preferred = new RealignmentResult();
var other = new RealignmentResult();
Assert.Equal(preferred, comparer.GetBetterResult(preferred, other));
Assert.Equal(other, comparer.GetBetterResult(other, preferred));
Assert.Equal(preferred, comparer.GetBetterResult(preferred, null));
Assert.Equal(preferred, comparer.GetBetterResult(null, preferred));
Assert.Equal(null, comparer.GetBetterResult(null, null));
preferred.NumMismatches = 5;
Assert.Equal(other, comparer.GetBetterResult(preferred, other));
}
public void CompareAlignments()
{
var comparer = new BasicAlignmentComparer();
var perfect = new AlignmentSummary();
var otherPerfect = new AlignmentSummary();
var oneMismatch = new AlignmentSummary();
oneMismatch.NumMismatches = 1;
var oneIndel = new AlignmentSummary();
oneIndel.NumIndels = 1;
var oneIndelOneMismatch = new AlignmentSummary();
oneIndelOneMismatch.NumMismatches = 1;
oneIndelOneMismatch.NumIndels = 1;
Assert.Equal(1, comparer.CompareAlignments(perfect, null));
// indels =, mismatch =, 0
Assert.Equal(0, comparer.CompareAlignments(perfect, otherPerfect));
// indels =, mismatch <, 1
Assert.Equal(1, comparer.CompareAlignments(perfect, oneMismatch));
// indels =, mismatch >, -1
Assert.Equal(-1, comparer.CompareAlignments(oneMismatch, perfect));
// indels <, mismatch =, 1
Assert.Equal(1, comparer.CompareAlignments(perfect, oneIndel));
// indels <, mismatch <, 1
Assert.Equal(1, comparer.CompareAlignments(oneIndel, oneIndelOneMismatch));
// indels <, mismatch >, -1
Assert.Equal(-1, comparer.CompareAlignments(oneMismatch, oneIndel));
// indels >, mismatch =, -1
Assert.Equal(-1, comparer.CompareAlignments(oneIndel, perfect));
// indels >, mismatch <, 1
Assert.Equal(1, comparer.CompareAlignments(oneIndel, oneIndelOneMismatch));
// indels >, mismatch >, -1
Assert.Equal(-1, comparer.CompareAlignments(oneIndelOneMismatch, perfect));
var twoIndels = new AlignmentSummary()
{
NumIndels = 2, NumMismatches = 0
};
var twoMismatches = new AlignmentSummary()
{
NumIndels = 0, NumMismatches = 2
};
// 1 mismatch and 0 indels in first, 2 indels and 0 mismatches in second, favor the first
Assert.Equal(1, comparer.CompareAlignments(oneMismatch, twoIndels));
// 1 mismatch and 0 indels in first, 1 indel in second, favor the second
Assert.Equal(-1, comparer.CompareAlignments(oneMismatch, oneIndel));
// 2 mismatches and 0 indels in first, 2 indels in second, favor the second -- special rule only applies to single-mismatch reads (with no indels)
Assert.Equal(-1, comparer.CompareAlignments(twoMismatches, twoIndels));
// 1 mismatch and 1 indel in first, 2 indels and 0 mismatches in second, favor the second -- special rule only applies to single-mismatch reads (with no indels)
Assert.Equal(-1, comparer.CompareAlignments(oneIndelOneMismatch, twoIndels));
var oneMismatchOneSoftclip = new AlignmentSummary()
{
NumNonNSoftclips = 1, NumMismatches = 1
};
var oneSoftclip = new AlignmentSummary()
{
NumNonNSoftclips = 1
};
var oneIndelOneSoftclip = new AlignmentSummary()
{
NumIndels = 1, NumNonNSoftclips = 1
};
// 1 mismatch and 1 softclip, 0 mismatch and 1 softclip, favor the second
Assert.Equal(-1, comparer.CompareAlignments(oneMismatchOneSoftclip, oneSoftclip));
// 1 mismatch and 0 softclip, 0 mimatch and 1 softclip, favor the second
Assert.Equal(-1, comparer.CompareAlignments(oneMismatch, oneSoftclip));
// 0 mismatch and 0 softclip, 0 mismatch and 1 softclip, favor the first
Assert.Equal(1, comparer.CompareAlignments(perfect, oneSoftclip));
// 1 indel and 0 mismatch/sc, 1 indel and 1 softclip, favor the first
Assert.Equal(1, comparer.CompareAlignments(oneIndel, oneIndelOneSoftclip));
// 2 indel and 0 mismatch/sc, 1 indel and 1 softclip, favor the first
Assert.Equal(1, comparer.CompareAlignments(twoIndels, oneIndelOneSoftclip));
// 1 indel and 0 mismatch/sc, 0 indel and 1 softclip, favor the first
Assert.Equal(1, comparer.CompareAlignments(oneIndel, oneSoftclip));
// 2 indel and 0 mismatch/sc, 0 indel and 1 softclip, favor the first
Assert.Equal(1, comparer.CompareAlignments(twoIndels, oneSoftclip));
}
public void CompareAlignmentsWithOriginal()
{
var comparer = new BasicAlignmentComparer();
var perfect = new AlignmentSummary();
var otherPerfect = new AlignmentSummary();
var oneMismatch = new AlignmentSummary();
oneMismatch.NumMismatchesIncludeSoftclip = 1;
var oneIndel = new AlignmentSummary();
oneIndel.NumIndels = 1;
var oneIndel2 = new AlignmentSummary();
oneIndel2.NumIndels = 1;
var oneIndelOneMismatch = new AlignmentSummary();
oneIndelOneMismatch.NumMismatchesIncludeSoftclip = 1;
oneIndelOneMismatch.NumIndels = 1;
var twoIndels = new AlignmentSummary()
{
NumIndels = 2, NumMismatchesIncludeSoftclip = 0
};
var twoIndels2 = new AlignmentSummary()
{
NumIndels = 2, NumMismatchesIncludeSoftclip = 0
};
var twoMismatches = new AlignmentSummary()
{
NumIndels = 0, NumMismatchesIncludeSoftclip = 2
};
Assert.Equal(1, comparer.CompareAlignmentsWithOriginal(perfect, null));
// --------------
// realignment has zero mismatch
// --------------
// both perfect, pick original
Assert.Equal(-1, comparer.CompareAlignmentsWithOriginal(perfect, otherPerfect));
// indels both 0, mismatch smaller by 1, pick new
Assert.Equal(1, comparer.CompareAlignmentsWithOriginal(perfect, oneMismatch));
// special rule for one indel vs. one mismatch , pick original
Assert.Equal(-1, comparer.CompareAlignmentsWithOriginal(oneIndel, oneMismatch));
// gain one indel, mismatch both 0, pick original
Assert.Equal(-1, comparer.CompareAlignmentsWithOriginal(oneIndel, perfect));
// gain one indel, mismatch smaller by 2, pick new
Assert.Equal(1, comparer.CompareAlignmentsWithOriginal(oneIndel, twoMismatches));
// indels both 1, mismatch both 0, pick new
Assert.Equal(1, comparer.CompareAlignmentsWithOriginal(oneIndel, oneIndel2));
// indels both 1, mismatch smaller by 1, pick new
Assert.Equal(1, comparer.CompareAlignmentsWithOriginal(oneIndel, oneIndelOneMismatch));
// special rule doesn't apply to two indels, pick new
Assert.Equal(1, comparer.CompareAlignmentsWithOriginal(twoIndels, oneMismatch));
// gain two indels, mismatch both 0, pick original
Assert.Equal(-1, comparer.CompareAlignmentsWithOriginal(twoIndels, perfect));
// gain two indels, mismatch smaller by 2, pick new
Assert.Equal(1, comparer.CompareAlignmentsWithOriginal(twoIndels, twoMismatches));
// indels both 2, mismatch both 0, pick new
Assert.Equal(1, comparer.CompareAlignmentsWithOriginal(twoIndels, twoIndels2));
// gain one indel, mismatch smaller by 1, pick new
Assert.Equal(1, comparer.CompareAlignmentsWithOriginal(twoIndels, oneIndelOneMismatch));
// gain one indel, mismatch both 0, pick new
Assert.Equal(1, comparer.CompareAlignmentsWithOriginal(twoIndels, oneIndel));
// --------------
// realignment has >=1 mismatch
// --------------
// --------------
// short indels <= 3bp
// --------------
var shortIndelOneMismatchNew = new AlignmentSummary()
{
NumIndelBases = 3, NumIndels = 1, NumMismatchesIncludeSoftclip = 1, MismatchesIncludeSoftclip = new List <string> {
"5_A_C"
}
};
var shortIndelOneMismatchShared = new AlignmentSummary()
{
NumIndelBases = 3, NumIndels = 1, NumMismatchesIncludeSoftclip = 1, MismatchesIncludeSoftclip = new List <string> {
"3_A_C"
}
};
var zeroIndelWithFourMismatch = new AlignmentSummary()
{
NumMismatchesIncludeSoftclip = 4, MismatchesIncludeSoftclip = new List <string> {
"0_A_C", "1_A_C", "2_A_C", "3_A_C"
}
};
var zeroIndelWithThreeMismatch = new AlignmentSummary()
{
NumMismatchesIncludeSoftclip = 3, MismatchesIncludeSoftclip = new List <string> {
"1_A_C", "2_A_C", "3_A_C"
}
};
// realignment introduced a new mismatch, pick original
Assert.Equal(-1, comparer.CompareAlignmentsWithOriginal(shortIndelOneMismatchNew, zeroIndelWithFourMismatch));
// the one mismatch exists in both original and realignment, pick new
Assert.Equal(1, comparer.CompareAlignmentsWithOriginal(shortIndelOneMismatchShared, zeroIndelWithFourMismatch));
// reduction of mismatch < 3, pick original
Assert.Equal(-1, comparer.CompareAlignmentsWithOriginal(shortIndelOneMismatchShared, zeroIndelWithThreeMismatch));
// --------------
// indels > 3bp
// --------------
var MediumIndelOneMismatchNew = new AlignmentSummary()
{
NumIndelBases = 4, NumIndels = 1, NumMismatchesIncludeSoftclip = 1, MismatchesIncludeSoftclip = new List <string> {
"5_A_C"
}
};
var MediumIndelOneMismatchShared = new AlignmentSummary()
{
NumIndelBases = 4, NumIndels = 1, NumMismatchesIncludeSoftclip = 1, MismatchesIncludeSoftclip = new List <string> {
"3_A_C"
}
};
var MediumIndelTwoMismatchBothNew = new AlignmentSummary()
{
NumIndelBases = 4, NumIndels = 1, NumMismatchesIncludeSoftclip = 2, MismatchesIncludeSoftclip = new List <string> {
"5_A_C", "6_A_C"
}
};
var MediumIndelTwoMismatchOneShared = new AlignmentSummary()
{
NumIndelBases = 4, NumIndels = 1, NumMismatchesIncludeSoftclip = 2, MismatchesIncludeSoftclip = new List <string> {
"2_A_C", "5_A_C"
}
};
var zeroIndelWithFiveMismatch = new AlignmentSummary()
{
NumMismatchesIncludeSoftclip = 5, MismatchesIncludeSoftclip = new List <string> {
"0_A_C", "1_A_C", "2_A_C", "3_A_C", "4_A_C"
}
};
// mismatch smaller by 2, realignment has one mismatch, shared with original, pick original
Assert.Equal(-1, comparer.CompareAlignmentsWithOriginal(MediumIndelOneMismatchShared, zeroIndelWithThreeMismatch));
// mismatch smaller by 3, realignment has one mismatch, shared with original, pick new
Assert.Equal(1, comparer.CompareAlignmentsWithOriginal(MediumIndelOneMismatchShared, zeroIndelWithFourMismatch));
// mismatch smaller by 2, realignment created 1 new mismatch, pick original
Assert.Equal(-1, comparer.CompareAlignmentsWithOriginal(MediumIndelOneMismatchNew, zeroIndelWithThreeMismatch));
// mismatch smaller by 3, realignment created 1 new mismatch, pick new
Assert.Equal(1, comparer.CompareAlignmentsWithOriginal(MediumIndelOneMismatchNew, zeroIndelWithFourMismatch));
// mismatch smaller by 3, but realignment created 2 new mismatches, pick original
Assert.Equal(-1, comparer.CompareAlignmentsWithOriginal(MediumIndelTwoMismatchBothNew, zeroIndelWithFiveMismatch));
// mismatch smaller by 3, realignment has two mismatches, one introduced by indel, pick new
Assert.Equal(1, comparer.CompareAlignmentsWithOriginal(MediumIndelTwoMismatchOneShared, zeroIndelWithFiveMismatch));
// mismatch smaller by 2, realignment has two mismatches, one introduced by indel, pick original
Assert.Equal(-1, comparer.CompareAlignmentsWithOriginal(MediumIndelTwoMismatchOneShared, zeroIndelWithFourMismatch));
var LongIndelOneMismatchShared = new AlignmentSummary()
{
NumIndelBases = 9, NumIndels = 1, NumMismatchesIncludeSoftclip = 1, MismatchesIncludeSoftclip = new List <string> {
"5_A_C"
}
};
var LongIndelTwoMismatchOneShared = new AlignmentSummary()
{
NumIndelBases = 9, NumIndels = 1, NumMismatchesIncludeSoftclip = 2, MismatchesIncludeSoftclip = new List <string> {
"2_A_C", "5_A_C"
}
};
var LongIndelTwoMismatchBothNew = new AlignmentSummary()
{
NumIndelBases = 9, NumIndels = 1, NumMismatchesIncludeSoftclip = 2, MismatchesIncludeSoftclip = new List <string> {
"5_A_C", "6_A_C"
}
};
var HighFrequencyIndelOneMismatchShared = new AlignmentSummary()
{
NumIndelBases = 4, NumIndels = 1, HasHighFrequencyIndel = true, NumMismatchesIncludeSoftclip = 1, MismatchesIncludeSoftclip = new List <string> {
"5_A_C"
}
};
var HighFrequencyIndelTwoMismatchOneShared = new AlignmentSummary()
{
NumIndelBases = 4, NumIndels = 1, HasHighFrequencyIndel = true, NumMismatchesIncludeSoftclip = 2, MismatchesIncludeSoftclip = new List <string> {
"2_A_C", "5_A_C"
}
};
var HighFrequencyIndelTwoMismatchBothNew = new AlignmentSummary()
{
NumIndelBases = 9, NumIndels = 1, NumMismatchesIncludeSoftclip = 2, MismatchesIncludeSoftclip = new List <string> {
"5_A_C", "6_A_C"
}
};
var zeroIndelWithTwoMismatch = new AlignmentSummary()
{
NumMismatchesIncludeSoftclip = 2, MismatchesIncludeSoftclip = new List <string> {
"1_A_C", "2_A_C"
}
};
// mismatch smaller by 2 (3->1), realignment has one mismatch, shared with original, pick new
Assert.Equal(1, comparer.CompareAlignmentsWithOriginal(LongIndelOneMismatchShared, zeroIndelWithThreeMismatch));
// mismatch smaller by 1 (2->1), realignment has one mismatch, shared with original, pick original
Assert.Equal(-1, comparer.CompareAlignmentsWithOriginal(LongIndelOneMismatchShared, zeroIndelWithTwoMismatch));
// mismatch smaller by 2 (4->2), realignment has two mismatches, one introduced by indel, pick new
Assert.Equal(1, comparer.CompareAlignmentsWithOriginal(LongIndelTwoMismatchOneShared, zeroIndelWithFourMismatch));
// mismatch smaller by 1 (3->2), realignment has two mismatches, one introduced by indel, pick original
Assert.Equal(-1, comparer.CompareAlignmentsWithOriginal(LongIndelTwoMismatchOneShared, zeroIndelWithThreeMismatch));
// mismatch smaller by 2 (4->2), but realignment created 2 new mismatches, pick original
Assert.Equal(-1, comparer.CompareAlignmentsWithOriginal(LongIndelTwoMismatchBothNew, zeroIndelWithFourMismatch));
// mismatch smaller by 2 (3->1), realignment has one mismatch, shared with original, pick new
Assert.Equal(1, comparer.CompareAlignmentsWithOriginal(HighFrequencyIndelOneMismatchShared, zeroIndelWithThreeMismatch));
// mismatch smaller by 1 (2->1), realignment has one mismatch, shared with original, pick original
Assert.Equal(-1, comparer.CompareAlignmentsWithOriginal(HighFrequencyIndelOneMismatchShared, zeroIndelWithTwoMismatch));
// mismatch smaller by 2 (4->2), realignment has two mismatches, one introduced by indel, pick new
Assert.Equal(1, comparer.CompareAlignmentsWithOriginal(HighFrequencyIndelTwoMismatchOneShared, zeroIndelWithFourMismatch));
// mismatch smaller by 1 (3->2), realignment has two mismatches, one introduced by indel, pick original
Assert.Equal(-1, comparer.CompareAlignmentsWithOriginal(HighFrequencyIndelTwoMismatchOneShared, zeroIndelWithThreeMismatch));
// mismatch smaller by 2 (4->2), but realignment created 2 new mismatches, pick original
Assert.Equal(-1, comparer.CompareAlignmentsWithOriginal(HighFrequencyIndelTwoMismatchBothNew, zeroIndelWithFourMismatch));
}
