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Feature/rebase 3.6.2 (#592)
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* Disabled left-alignment of variants in legacy VID mode. (#505)

* Disabled left-alignment of variants in legacy VID mode.

* Added some unit tests to check the left alignment behavior between normal and legacy VID mode.

* Updated the ReSharper settings to properly set var behavior.

* Fixed the LOH VID issue in CNVs (#503)

* Fixed the parsing issue when encountering reference sequences with colons. (#494)

* Updating the version

* Updated Nirvana to avoid using the bidirectional trimmer on translocations when using the legacy VID option. (#507)

* Added HLA reference parsing to the legacy variant ID parser. (#508)

* Reverted some files that had their permissions changed

* Revert "Reverted some files that had their permissions changed"

This reverts commit d9e3ffea6c34829c9db372fbe8014b62ed412694.

* Minor cleanup with file permissions

* Minor ReSharper changes

* Removed unnecessary comments in LegacyVariantId
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Stromberg, Michael authored and GitHub Enterprise committed Jun 2, 2021
1 parent a62a4f8 commit a8b2bac
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Empty file modified UnitTests/Downloader/ConfigurationTests.cs
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98 changes: 59 additions & 39 deletions UnitTests/Vcf/VariantCreator/LegacyVariantIdTests.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -9,69 +9,89 @@ namespace UnitTests.Vcf.VariantCreator
{
public sealed class LegacyVariantIdTests
{
private readonly LegacyVariantId _vidCreator = new LegacyVariantId(ChromosomeUtilities.RefNameToChromosome);
private readonly LegacyVariantId _vidCreator = new(ChromosomeUtilities.RefNameToChromosome);

[Theory]
[InlineData(66507, 66507, "T", "A", "1:66507:A")]
[InlineData(66522, 66521, "", "ATATA", "1:66522:66521:ATATA")]
[InlineData(66573, 66574, "TA", "", "1:66573:66574")]
[InlineData(66573, 66572, "", "TACTATATATTA", "1:66573:66572:TACTATATATTA")]
[InlineData(100, 104, "TAGGT", "ACTTA", "1:100:104:ACTTA")]
[InlineData(100, 104, "TAGGT", "", "1:100:104")]
[InlineData(101, 100, "", "CGA", "1:101:100:CGA")]
[InlineData(100, 100, "T", "A", "1:100:A")]
[InlineData(100, 104, "TAGGT", "CGA", "1:100:104:CGA")]
[InlineData(100, 99, "", "ACTGACGTACGAAGTTGCCGTACGTACTTGTCC", "1:100:99:3bd631d37e62d5db0f6d5d6db3cdcb60")]
[InlineData(66366, 66378, "ATATAATATATAA", "TATATATATTATTATATAATATAATATATATTATATAATATATTTTATTATATAATATAATATATATTATATAATATAATATATTTTATTATATAAATATATATTATATTATATAATATAATATATATTAATATAAATATATATTAT", "1:66366:66378:17b72647da13e3c186348467b29b0492")]
[InlineData(66507, 66507, "T", "A", "1:66507:A")]
[InlineData(66522, 66521, "", "ATATA", "1:66522:66521:ATATA")]
[InlineData(66573, 66574, "TA", "", "1:66573:66574")]
[InlineData(66573, 66572, "", "TACTATATATTA", "1:66573:66572:TACTATATATTA")]
[InlineData(100, 104, "TAGGT", "ACTTA", "1:100:104:ACTTA")]
[InlineData(100, 104, "TAGGT", "", "1:100:104")]
[InlineData(101, 100, "", "CGA", "1:101:100:CGA")]
[InlineData(100, 100, "T", "A", "1:100:A")]
[InlineData(100, 104, "TAGGT", "CGA", "1:100:104:CGA")]
[InlineData(100, 99, "", "ACTGACGTACGAAGTTGCCGTACGTACTTGTCC", "1:100:99:3bd631d37e62d5db0f6d5d6db3cdcb60")]
[InlineData(66366, 66378, "ATATAATATATAA",
"TATATATATTATTATATAATATAATATATATTATATAATATATTTTATTATATAATATAATATATATTATATAATATAATATATTTTATTATATAAATATATATTATATTATATAATATAATATATATTAATATAAATATATATTAT",
"1:66366:66378:17b72647da13e3c186348467b29b0492")]
[InlineData(100, 300, "", "<M>", "1:100:*")]
public void Create_SmallVariants_ReturnVid(int start, int end, string refAllele, string altAllele, string expectedVid)
{
string observedVid = _vidCreator.Create(null, VariantCategory.SmallVariant, null, ChromosomeUtilities.Chr1, start, end, refAllele, altAllele, null);
string observedVid = _vidCreator.Create(null, VariantCategory.SmallVariant, null, ChromosomeUtilities.Chr1, start, end, refAllele,
altAllele, null);
Assert.Equal(expectedVid, observedVid);
}

[Theory]
[InlineData(66507, 66507, "T", ".", "1:66507:66507:T")]
[InlineData(100, 100, "T", "T", "1:100:100:T")]
[InlineData(100, 100, "T", ".", "1:100:100:T")]
[InlineData(100, 100, "T", "T", "1:100:100:T")]
[InlineData(100, 100, "T", ".", "1:100:100:T")]
public void Create_Reference_ReturnVid(int start, int end, string refAllele, string altAllele, string expectedVid)
{
string observedVid = _vidCreator.Create(null, VariantCategory.Reference, null, ChromosomeUtilities.Chr1, start, end, refAllele, altAllele, null);
string observedVid = _vidCreator.Create(null, VariantCategory.Reference, null, ChromosomeUtilities.Chr1, start, end, refAllele, altAllele,
null);
Assert.Equal(expectedVid, observedVid);
}

[Fact]
public void Create_TranslocationBreakend_ReturnVid()
[Theory]
[InlineData(2617277, "A", "AAAAAAAAAAAAAAAAAATTAGTCAGGCAC[chr3:153444911[", "2:2617277:+:3:153444911:+")]
[InlineData(32973490, "T", "T]chr9:74198768]", "2:32973490:+:9:74198768:-")]
[InlineData(321681, "G", "G[13:123460[", "2:321681:+:13:123460:+")]
[InlineData(32527769, "C", "[HLA-DRB1*13:02:01:3117[C", "2:32527769:-:HLA-DRB1*13:02:01:3117:+")]
public void Create_TranslocationBreakend_ReturnVid(int position, string refAllele, string altAllele, string expectedVid)
{
string observedVid = _vidCreator.Create(null, VariantCategory.SV, "BND", ChromosomeUtilities.Chr2, 321681, 321681, "G", "G[13:123460[", null);
Assert.Equal("2:321681:+:13:123460:+", observedVid);
string observedVid = _vidCreator.Create(null, VariantCategory.SV, "BND", ChromosomeUtilities.Chr2, position, position, refAllele,
altAllele, null);
Assert.Equal(expectedVid, observedVid);
}

[Theory]
[InlineData(1000, 3001000, "<ROH>", null, "ROH", VariantCategory.ROH, "1:1001:3001000:ROH")]
[InlineData(1350082, 1351320, "<DEL>", null, "DEL", VariantCategory.SV, "1:1350083:1351320")]
[InlineData(999, 2015, "<DUP>", null, "DUP", VariantCategory.SV, "1:1000:2015:DUP")]
[InlineData(1477854, 1477984, "<DUP:TANDEM>", null, "DUP", VariantCategory.SV, "1:1477855:1477984:TDUP")]
[InlineData(1477968, 1477968, "<INS>", null, "INS", VariantCategory.SV, "1:1477969:1477968:INS")]
[InlineData(2000, 5000, "<CNV>", null, "CNV", VariantCategory.CNV, "1:2001:5000:CNV")]
[InlineData(2000, 5000, "<CN3>", null, "CNV", VariantCategory.CNV, "1:2001:5000:CN3")]
[InlineData(2000, 5000, "<DUP>", null, "CNV", VariantCategory.CNV, "1:2001:5000:CDUP")]
[InlineData(2000, 5000, "<DEL>", null, "CNV", VariantCategory.CNV, "1:2001:5000:CDEL")]
[InlineData(2000, 5000, "<ALU>", null, "ALU", VariantCategory.SV, "1:2001:5000:MEI")]
[InlineData(2000, 5000, "<LINE1>", null, "LINE1", VariantCategory.SV, "1:2001:5000:MEI")]
[InlineData(2000, 5000, "<SVA>", null, "SVA", VariantCategory.SV, "1:2001:5000:MEI")]
[InlineData(2000, 5000, "<BOB>", null, "BOB", VariantCategory.SV, "1:2001:5000")]
[InlineData(1715898, 1750149, "<DUP>", null, "CNV", VariantCategory.CNV, "1:1715899:1750149:CDUP")]
[InlineData(2650426, 2653074, "<DEL>", null, "CNV", VariantCategory.CNV, "1:2650427:2653074:CDEL")]
[InlineData(321682, 421681, "<INV>", null, "INV", VariantCategory.SV, "1:321683:421681:Inverse")]
[InlineData(199, 202, "<STR5>", "TTG", "", VariantCategory.RepeatExpansion, "1:200:202:TTG:5")]
public void Create_StructuralVariants_ReturnVid(int start, int end, string altAllele, string repeatUnit,
string svType, VariantCategory category, string expectedVid)
[InlineData(1000, 3001000, "<ROH>", null, "ROH", VariantCategory.ROH, "1:1001:3001000:ROH")]
[InlineData(1350082, 1351320, "<DEL>", null, "DEL", VariantCategory.SV, "1:1350083:1351320")]
[InlineData(999, 2015, "<DUP>", null, "DUP", VariantCategory.SV, "1:1000:2015:DUP")]
[InlineData(1477854, 1477984, "<DUP:TANDEM>", null, "DUP", VariantCategory.SV, "1:1477855:1477984:TDUP")]
[InlineData(1477968, 1477968, "<INS>", null, "INS", VariantCategory.SV, "1:1477969:1477968:INS")]
[InlineData(2000, 5000, "<CNV>", null, "CNV", VariantCategory.CNV, "1:2001:5000:CNV")]
[InlineData(2000, 5000, "<CN3>", null, "CNV", VariantCategory.CNV, "1:2001:5000:CN3")]
[InlineData(2000, 5000, "<DUP>", null, "CNV", VariantCategory.CNV, "1:2001:5000:CDUP")]
[InlineData(2000, 5000, "<DEL>", null, "CNV", VariantCategory.CNV, "1:2001:5000:CDEL")]
[InlineData(2000, 5000, "<ALU>", null, "ALU", VariantCategory.SV, "1:2001:5000:MEI")]
[InlineData(2000, 5000, "<LINE1>", null, "LINE1", VariantCategory.SV, "1:2001:5000:MEI")]
[InlineData(2000, 5000, "<SVA>", null, "SVA", VariantCategory.SV, "1:2001:5000:MEI")]
[InlineData(2000, 5000, "<BOB>", null, "BOB", VariantCategory.SV, "1:2001:5000")]
[InlineData(1715898, 1750149, "<DUP>", null, "CNV", VariantCategory.CNV, "1:1715899:1750149:CDUP")]
[InlineData(2650426, 2653074, "<DEL>", null, "CNV", VariantCategory.CNV, "1:2650427:2653074:CDEL")]
[InlineData(321682, 421681, "<INV>", null, "INV", VariantCategory.SV, "1:321683:421681:Inverse")]
[InlineData(199, 202, "<STR5>", "TTG", "", VariantCategory.RepeatExpansion, "1:200:202:TTG:5")]
public void Create_StructuralVariants_ReturnVid(int start, int end, string altAllele, string repeatUnit, string svType,
VariantCategory category, string expectedVid)
{
string observedVid = _vidCreator.Create(null, category, svType, ChromosomeUtilities.Chr1, start, end, "", altAllele, repeatUnit);
Assert.Equal(expectedVid, observedVid);
}

[Fact]
public void Create_LOH_ReturnsCnvVid()
{
const string altAllele = "<CNV>";
const string svType = "LOH";
VariantCategory variantCategory = VariantFactory.GetVariantCategory(altAllele, svType);

string observedVid = _vidCreator.Create(null, variantCategory, svType, ChromosomeUtilities.Chr1, 787923, 887923, "N", altAllele, null);
Assert.Equal("1:787924:887923:CNV", observedVid);
}

[Fact]
public void GetSmallVariantVid_UnknownVariantType_ThrowsException()
{
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