public void IsReadClippedAtMNVSite_NoSoftclips()
{
IMNVSoftClipReadFilter scReadFilter = new MNVSoftClipReadFilter();
// SNV:
// pos |15 20
// ref |ACTGAGACTGA
// alt |ACTGAAACTGA
var snv = TestHelper.CreateDummyAllele("chr1", 20, "G", "A", 2000, 50);
var del = TestHelper.CreateDummyAllele("chr1", 20, "GAC", "G", 2000, 50);
var ins = TestHelper.CreateDummyAllele("chr1", 20, "G", "GTA", 2000, 50);
var homopolymerDel = TestHelper.CreateDummyAllele("chr1", 20, "GGGGG", "G", 2000, 50);
var homopolymerIns = TestHelper.CreateDummyAllele("chr1", 20, "G", "GGGGG", 2000, 50);
// Read is ref haplotype (11M)
var refRead = TestHelper.CreateRead("chr1", "ACTGAGACTGA", 15, new CigarAlignment("11M"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(refRead, snv));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(refRead, del));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(refRead, ins));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(refRead, homopolymerDel));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(refRead, homopolymerIns));
// Read contains mismatch, insertion, or deletion (no clipping)
// Mismatch
// pos |15 20
// ref |ACTGAGACTGA
// read |ACTGAAACTGA
var mismatchRead = TestHelper.CreateRead("chr1", "ACTGAAACTGA", 15, new CigarAlignment("5M1X5M")); // 20: G > A
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(mismatchRead, snv));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(mismatchRead, del));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(mismatchRead, ins));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(mismatchRead, homopolymerDel));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(mismatchRead, homopolymerIns));
// Deletion
// pos |15 20
// ref |ACTGAGACTGA
// read |ACTGAG--TGA
var delRead = TestHelper.CreateRead("chr1", "ACTGAGTGA", 15, new CigarAlignment("6M2D3M")); // 20: GAC > G
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(delRead, snv));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(delRead, del));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(delRead, ins));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(delRead, homopolymerDel));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(delRead, homopolymerIns));
// Insertion
// pos |15 20
// ref |ACTGAG--ACTGA
// read |ACTGAGTGACTGA
var insRead = TestHelper.CreateRead("chr1", "ACTGAGTGACTGA", 15, new CigarAlignment("6M2I5M")); // 20: G>GTG
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(insRead, snv));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(insRead, del));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(insRead, ins));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(insRead, homopolymerDel));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(insRead, homopolymerIns));
}
public void IsReadClippedAtMNVSite_SNV()
{
IMNVSoftClipReadFilter scReadFilter = new MNVSoftClipReadFilter();
// SNV:
// pos |15 20
// ref |ACTGAGACTGA
// alt |ACTGAAACTGA
var snv = TestHelper.CreateDummyAllele("chr1", 20, "G", "A", 2000, 50);
// Corner cases for SNV
// startsWith5S
// pos |15 20
// snvRead |ACTGAAACTGA
// cigar |SSSSSXMMMMM
var startsWith5S = TestHelper.CreateRead("chr1", "ACTGAAACTGA", 20, new CigarAlignment("5S1X5M"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(startsWith5S, snv));
// startsWith6S
// pos |15 20
// snvRead |ACTGAAACTGA
// cigar |SSSSSSMMMMM
var startsWith6S = TestHelper.CreateRead("chr1", "ACTGAAACTGA", 21, new CigarAlignment("6S5M"));
Assert.Equal((true, false), scReadFilter.IsReadClippedAtMNVSite(startsWith6S, snv));
// startsWith7S
// pos |15 20
// snvRead |ACTGAAACTGA
// cigar |SSSSSSSMMMM
var startsWith7S = TestHelper.CreateRead("chr1", "ACTGAAACTGA", 22, new CigarAlignment("7S4M"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(startsWith7S, snv));
// endsWith5S
// pos |15 20
// snvRead |ACTGAAACTGA
// cigar |MMMMMXSSSSS
var endsWith5S = TestHelper.CreateRead("chr1", "ACTGAAACTGA", 15, new CigarAlignment("5M1X5S"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(endsWith5S, snv));
// endsWith6S
// pos |15 20
// snvRead |ACTGAAACTGA
// cigar |MMMMMSSSSSS
var endsWith6S = TestHelper.CreateRead("chr1", "ACTGAAACTGA", 15, new CigarAlignment("5M6S"));
Assert.Equal((false, true), scReadFilter.IsReadClippedAtMNVSite(endsWith6S, snv));
// endsWith7S
// pos |15 20
// snvRead |ACTGAAACTGA
// cigar |MMMMSSSSSSS
var endsWith7S = TestHelper.CreateRead("chr1", "ACTGAAACTGA", 15, new CigarAlignment("4M7S"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(endsWith7S, snv));
}
public void IsReadClippedAtMNVSite_HomopolymerIns()
{
IMNVSoftClipReadFilter scReadFilter = new MNVSoftClipReadFilter();
// Homopolymer insertion:
// pos |15 20
// ref |ACTGAG----ACTGA
// alt |ACTGAGGGGGACTGA
var homopolymerIns = TestHelper.CreateDummyAllele("chr1", 20, "G", "GGGGG", 2000, 50);
// Corner cases for Homopolymer run Insertion
// hinsStartsWith8S
// pos |15 20
// ref |ACTGA----GACTGA
// hinsRead |ACTGAGGGGGACTGA // alignment with visible indel
// hinsRead |ACTGAGGGGGACTGA // alignment with clipping
// cigar |SSSSSSSSXMMMMMM
var hinsStartsWith8S = TestHelper.CreateRead("chr1", "ACTGAGGGGGACTGA", 19, new CigarAlignment("8S1X6M"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(hinsStartsWith8S, homopolymerIns));
// hinsStartsWith9S
// pos |15 20
// ref |ACTGA----GACTGA
// hinsRead |ACTGAGGGGGACTGA // alignment with visible indel
// hinsRead |ACTGAGGGGGACTGA // alignment with clipping
// cigar |SSSSSSSSSMMMMMM
var hinsStartsWith9S = TestHelper.CreateRead("chr1", "ACTGAGGGGGACTGA", 20, new CigarAlignment("9S6M"));
Assert.Equal((true, false), scReadFilter.IsReadClippedAtMNVSite(hinsStartsWith9S, homopolymerIns));
// hinsStartsWith10S
// pos |15 20
// ref |ACTGA----GACTGA
// hinsRead |ACTGAGGGGGACTGA // alignment with visible indel
// hinsRead |ACTGAGGGGGACTGA // alignment with clipping
// cigar |SSSSSSSSSSMMMMM
var hinsStartsWith10S = TestHelper.CreateRead("chr1", "ACTGAGGGGGACTGA", 21, new CigarAlignment("10S5M"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(hinsStartsWith10S, homopolymerIns));
// hinsEndsWith8S
// pos |15 20
// ref |ACTGAG----ACTGA
// hinsRead |ACTGAGGGGGACTGA // alignment with visible indel
// hinsRead |ACTGAGGGGGACTGA // alignment with clipping
// cigar |MMMMMMXSSSSSSSS
var hinsEndsWith8S = TestHelper.CreateRead("chr1", "ACTGAGGGGGACTGA", 15, new CigarAlignment("6M1X8S"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(hinsEndsWith8S, homopolymerIns));
// hinsEndsWith9S
// pos |15 20
// ref |ACTGAG----ACTGA
// hinsRead |ACTGAGGGGGACTGA // alignment with visible indel
// hinsRead |ACTGAGGGGGACTGA // alignment with clipping
// cigar |MMMMMMSSSSSSSSS
var hinsEndsWith9S = TestHelper.CreateRead("chr1", "ACTGAGGGGGACTGA", 15, new CigarAlignment("6M9S"));
Assert.Equal((false, true), scReadFilter.IsReadClippedAtMNVSite(hinsEndsWith9S, homopolymerIns));
// hinsEndsWith10S
// pos |15 20
// ref |ACTGAG----ACTGA
// hinsRead |ACTGAGGGGGACTGA // alignment with visible indel
// hinsRead |ACTGAGGGGGACTGA // alignment with clipping
// cigar |MMMMMSSSSSSSSSS
var hinsEndsWith10S = TestHelper.CreateRead("chr1", "ACTGAGGGGGACTGA", 15, new CigarAlignment("5M10S"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(hinsEndsWith10S, homopolymerIns));
}
public void IsReadClippedAtMNVSite_HomopolymerDel()
{
IMNVSoftClipReadFilter scReadFilter = new MNVSoftClipReadFilter();
// Homopolymer deletion:
// pos |15 20
// ref |ACTGAGGGGGACTGA
// alt |ACTGAG----ACTGA
var homopolymerDel = TestHelper.CreateDummyAllele("chr1", 20, "GGGGG", "G", 2000, 50);
// Corner cases for Deletion in Homopolymer run
// hdelStartsWith4S
// pos |15 20
// ref |ACTGAGGGGGACTGA
// hdelRead |ACTGA----GACTGA // alignment with visible indel
// hdelRead | ACTGAGACTGA // alignment with clipping
// cigar | SSSSXMMMMMM
var hdelStartsWith4S = TestHelper.CreateRead("chr1", "ACTGAGACTGA", 23, new CigarAlignment("4S1X6M"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(hdelStartsWith4S, homopolymerDel));
// hdelStartsWith5S
// pos |15 20
// ref |ACTGAGGGGGACTGA
// hdelRead |ACTGA----GACTGA // alignment with visible indel
// hdelRead | ACTGAGACTGA // alignment with clipping
// cigar | SSSSSMMMMMM
var hdelStartsWith5S = TestHelper.CreateRead("chr1", "ACTGAGACTGA", 24, new CigarAlignment("5S6M"));
Assert.Equal((true, false), scReadFilter.IsReadClippedAtMNVSite(hdelStartsWith5S, homopolymerDel));
// hdelStartsWith6S
// pos |15 20
// ref |ACTGAGGGGGACTGA
// hdelRead |ACTGA----GACTGA // alignment with visible indel
// hdelRead | ACTGAGACTGA // alignment with clipping
// cigar | SSSSSSMMMMM
var hdelStartsWith6S = TestHelper.CreateRead("chr1", "ACTGAGACTGA", 25, new CigarAlignment("6S5M"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(hdelStartsWith6S, homopolymerDel));
// hdelEndssWith4S
// pos |15 20
// ref |ACTGAGGGGGACTGA
// hdelRead |ACTGAG----ACTGA // alignment with visible indel
// hdelRead |ACTGAGACTGA // alignment with clipping
// cigar |MMMMMMXSSSS
var hdelEndssWith4S = TestHelper.CreateRead("chr1", "ACTGAGACTGA", 15, new CigarAlignment("6M1X4S"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(hdelEndssWith4S, homopolymerDel));
// hdelEndssWith5S
// pos |15 20
// ref |ACTGAGGGGGACTGA
// hdelRead |ACTGAG----ACTGA // alignment with visible indel
// hdelRead |ACTGAGACTGA // alignment with clipping
// cigar |MMMMMMSSSSS
var hdelEndssWith5S = TestHelper.CreateRead("chr1", "ACTGAGACTGA", 15, new CigarAlignment("6M5S"));
Assert.Equal((false, true), scReadFilter.IsReadClippedAtMNVSite(hdelEndssWith5S, homopolymerDel));
// hdelEndssWith6S
// pos |15 20
// ref |ACTGAGGGGGACTGA
// hdelRead |ACTGAG----ACTGA // alignment with visible indel
// hdelRead |ACTGAGACTGA // alignment with clipping
// cigar |MMMMMSSSSSS
var hdelEndssWith6S = TestHelper.CreateRead("chr1", "ACTGAGACTGA", 15, new CigarAlignment("5M6S"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(hdelEndssWith6S, homopolymerDel));
}
public void IsReadClippedAtMNVSite_Ins()
{
IMNVSoftClipReadFilter scReadFilter = new MNVSoftClipReadFilter();
// SNV:
// pos |15 20
// ref |ACTGAGACTGA
var ins = TestHelper.CreateDummyAllele("chr1", 20, "G", "GTA", 2000, 50);
// Corner cases for insertion
// insStartsWith7S
// pos |15 20
// ref |ACTGAG--ACTGA
// insRead |ACTGAGTAACTGA // Correct alignment
// insRead |ACTGAGTAACTGA // Current alignment
// cigar |SSSSSSSXMMMMM
var insStartsWith7S = TestHelper.CreateRead("chr1", "ACTGAGTAACTGA", 20, new CigarAlignment("7S1X5M"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(insStartsWith7S, ins));
// insStartsWith8S
// pos |15 20
// ref |ACTGAG--ACTGA
// insRead |ACTGAGTAACTGA // Correct alignment
// insRead |ACTGAGTAACTGA // Current alignment
// cigar |SSSSSSSSMMMMM
var insStartsWith8S = TestHelper.CreateRead("chr1", "ACTGAGTAACTGA", 21, new CigarAlignment("8S5M"));
Assert.Equal((true, false), scReadFilter.IsReadClippedAtMNVSite(insStartsWith8S, ins));
// insStartsWith9S
// pos |15 20
// ref |ACTGAG--ACTGA
// insRead |ACTGAGTAACTGA // Correct alignment
// insRead |ACTGAGTAACTGA // Current alignment
// cigar |SSSSSSSSSMMMM
var insStartsWith9S = TestHelper.CreateRead("chr1", "ACTGAGTAACTGA", 22, new CigarAlignment("9S4M"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(insStartsWith9S, ins));
// insEndsWith6S
// pos |15 20
// ref |ACTGAG--ACTGA
// insRead |ACTGAGTAACTGA // Correct alignment
// insRead |ACTGAGTAACTGA // Current alignment
// cigar |MMMMMMXSSSSSS
var insEndsWith6S = TestHelper.CreateRead("chr1", "ACTGAGTAACTGA", 15, new CigarAlignment("6M1X6S"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(insEndsWith6S, ins));
// insEndsWith7S
// pos |15 20
// ref |ACTGAG--ACTGA
// insRead |ACTGAGTAACTGA // Correct alignment
// insRead |ACTGAGTAACTGA // Current alignment
// cigar |MMMMMMSSSSSSS
var insEndsWith7S = TestHelper.CreateRead("chr1", "ACTGAGTAACTGA", 15, new CigarAlignment("6M7S"));
Assert.Equal((false, true), scReadFilter.IsReadClippedAtMNVSite(insEndsWith7S, ins));
// insEndsWith8S
// pos |15 20
// ref |ACTGAG--ACTGA
// insRead |ACTGAGTAACTGA // Correct alignment
// insRead |ACTGAGTAACTGA // Current alignment
// cigar |MMMMMSSSSSSSS
var insEndsWith8S = TestHelper.CreateRead("chr1", "ACTGAGTAACTGA", 15, new CigarAlignment("5M8S"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(insEndsWith8S, ins));
// Reads that start and end with soft clip
// insEndsWith7SStartsWith3S (End clipping site matches MNV)
// pos | 15 20
// ref |ACTACTGAG--ACTGA
// insRead |CCCACTGAGTAACTGA // Correct alignment
// insRead |CCCACTGAGTAACTGA // Current alignment
// cigar |SSSMMMMMMSSSSSSS
var insEndsWith7SStartsWith3S = TestHelper.CreateRead("chr1", "CCCACTGAGTAACTGA", 15, new CigarAlignment("3S6M7S"));
Assert.Equal((false, true), scReadFilter.IsReadClippedAtMNVSite(insEndsWith7SStartsWith3S, ins));
// insStartsWith8SEndsWith3S (start clipping site matches MNV)
// pos |15 20
// ref |ACTGAG--ACTGAACT
// insRead |ACTGAGTAACTGACCC // Correct alignment
// insRead |ACTGAGTAACTGACCC // Current alignment
// cigar |SSSSSSSSMMMMMSSS
var insStartsWith8SEndsWith3S = TestHelper.CreateRead("chr1", "ACTGAGTAACTGACCC", 21, new CigarAlignment("8S5M3S"));
Assert.Equal((true, false), scReadFilter.IsReadClippedAtMNVSite(insStartsWith8SEndsWith3S, ins));
// insStartsWith7SEndsWith3S (neither clipping site matches MNV)
// pos |15 20
// ref |ACTGAG--ACTGAACT
// insRead |ACTGAGTAACTGACCC // Correct alignment
// insRead |ACTGAGTAACTGACCC // Current alignment
// cigar |SSSSSSSXMMMMMSSS
var insStartsWith7SEndsWith3S = TestHelper.CreateRead("chr1", "ACTGAGTAACTGACCC", 20, new CigarAlignment("7S1X5M3S"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(insStartsWith7SEndsWith3S, ins));
}
public void IsReadClippedAtMNVSite_Del()
{
IMNVSoftClipReadFilter scReadFilter = new MNVSoftClipReadFilter();
// SNV:
// pos |15 20
// ref |ACTGAGACTGA
var del = TestHelper.CreateDummyAllele("chr1", 20, "GAC", "G", 2000, 50);
// Corner cases for Deletion
// delStartsWith5S
// pos |15 20
// ref |ACTGAGACTGA
// delRead |ACTGAG--TGA // Correct alignment
// delRead | ACTGAGTGA // Current alignment
// cigar | SSSSSXMMM
var delStartsWith5S = TestHelper.CreateRead("chr1", "ACTGAGTGA", 22, new CigarAlignment("5S1X3M"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(delStartsWith5S, del));
// delStartsWith6S
// pos |15 20
// ref |ACTGAGACTGA
// delRead |ACTGAG--TGA // Correct alignment
// cigar | SSSSSSMMM
var delStartsWith6S = TestHelper.CreateRead("chr1", "ACTGAGTGA", 23, new CigarAlignment("6S3M"));
Assert.Equal((true, false), scReadFilter.IsReadClippedAtMNVSite(delStartsWith6S, del));
// delStartsWith7S
// pos |15 20
// ref |ACTGAGACTGA
// delRead |ACTGAG--TGA // Correct alignment
// delRead | ACTGAGTGA // Current alignment
// cigar | SSSSSSSMM
var delStartsWith7S = TestHelper.CreateRead("chr1", "ACTGAGTGA", 24, new CigarAlignment("7S2M"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(delStartsWith7S, del));
// delEndsWith4S
// pos |15 20
// ref |ACTGAGACTGA
// delRead |ACTGAG--TGA // Correct alignment
// delRead | ACTGAGTGA // Current alignment
// cigar | MMMMMSSSS
var delEndsWith4S = TestHelper.CreateRead("chr1", "ACTGAGTGA", 17, new CigarAlignment("5M4S"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(delEndsWith4S, del));
// delEndsWith5S
// pos |15 20
// ref |ACTGAGACTGA
// delRead |ACTGAG--TGA // Correct alignment
// delRead | ACTGAGTGA // Current alignment
// cigar | MMMMSSSSS
var delEndsWith5S = TestHelper.CreateRead("chr1", "ACTGAGTGA", 17, new CigarAlignment("4M5S"));
Assert.Equal((false, true), scReadFilter.IsReadClippedAtMNVSite(delEndsWith5S, del));
// delEndsWith6S
// pos |15 20
// ref |ACTGAGACTGA
// delRead |ACTGAG--TGA // Correct alignment
// delRead | ACTGAGTGA // Current alignment
// cigar | MMMSSSSSS
var delEndsWith6S = TestHelper.CreateRead("chr1", "ACTGAGTGA", 17, new CigarAlignment("3M6S"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(delEndsWith6S, del));
// Reads that start and end with soft clip
// delEndsWith5SStartsWith4S (End clipping site matches MNV)
// pos | 15 20
// ref |ACTGACTGAGACTGA
// delRead |CCCCACTGAG--TGA // Correct alignment
// delRead | CCCCACTGAGTGA // Current alignment
// cigar | SSSSMMMMSSSSS
var delEndsWith5SStartsWith4S = TestHelper.CreateRead("chr1", "CCCCACTGAGTGA", 17, new CigarAlignment("4S4M5S"));
Assert.Equal((false, true), scReadFilter.IsReadClippedAtMNVSite(delEndsWith5SStartsWith4S, del));
// delStartsWith6SEndsWith4S (Start clipping site matches MNV)
// pos |15 20
// ref |ACTGAGACTGAACTG
// delRead |ACTGAG--TGACCCC // Correct alignment
// cigar | SSSSSSMMMSSSS
var delStartsWith6SEndsWith4S = TestHelper.CreateRead("chr1", "ACTGAGTGACCCC", 23, new CigarAlignment("6S3M4S"));
Assert.Equal((true, false), scReadFilter.IsReadClippedAtMNVSite(delStartsWith6SEndsWith4S, del));
// delEndsWith6SStartsWith4S (neither clipping site matches MNV)
// pos | 15 20
// ref |ACTGACTGAGACTGA
// delRead |CCCCACTGAG--TGA // Correct alignment
// delRead | CCCCACTGAGTGA // Current alignment
// cigar | SSSSMMMSSSSSS
var delEndsWith6SStartsWith4S = TestHelper.CreateRead("chr1", "CCCCACTGAGTGA", 17, new CigarAlignment("4S3M6S"));
Assert.Equal((false, false), scReadFilter.IsReadClippedAtMNVSite(delEndsWith6SStartsWith4S, del));
}
