| Test |
Duration |
Result |
| testAreGencodeFuncotations[0]([TableFuncotation{dataSourceName='TEST', fieldMap={FIELD:VALUE}, altAllele=A}], false) |
0s |
passed |
| testAreGencodeFuncotations[1]([org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@86509ba7], true) |
0s |
passed |
| testAreGencodeFuncotations[2]([TableFuncotation{dataSourceName='TEST', fieldMap={FIELD:VALUE}, altAllele=A}, TableFuncotation{dataSourceName='TEST', fieldMap={FIELD2:VALUE1}, altAllele=A}], false) |
0s |
passed |
| testAreGencodeFuncotations[3]([org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@6ba11574, org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@c2bf0653], true) |
0s |
passed |
| testAreGencodeFuncotations[4]([org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@6ba11574, org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@c2bf0653, TableFuncotation{dataSourceName='TEST', fieldMap={FIELD:VALUE}, altAllele=A}], true) |
0s |
passed |
| testAreGencodeFuncotations[5]([TableFuncotation{dataSourceName='TEST', fieldMap={FIELD:VALUE}, altAllele=A}, org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@6ba11574, org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@c2bf0653], true) |
0s |
passed |
| testAssertValidStrand_InvalidStrands[0](null) |
0s |
passed |
| testAssertValidStrand_InvalidStrands[1](.) |
0s |
passed |
| testAssertValidStrand_ValidStrands[0](+) |
0s |
passed |
| testAssertValidStrand_ValidStrands[1](-) |
0s |
passed |
| testCreateFuncotations[0]([VC /tmp/funcotatorTmpFolder12282509861524526/GRCh37.p13.chr3.fasta @ chr3:1000000 Q. of type=SNP alleles=[A*, C] attr={BAZFIELD=BAZ, FOOFIELD=FOO} GT=[] filters=, VcfFuncotationMetadata{fieldNameToHeaderLineMap={FOOFIELD=INFO=<ID=FOOFIELD,Number=A,Type=String,Description="Description here">, BAZFIELD=INFO=<ID=BAZFIELD,Number=A,Type=String,Description="Description here">}}, TEST1) |
0.001s |
passed |
| testCreateFuncotations[1]([VC /tmp/funcotatorTmpFolder12282509861524526/GRCh37.p13.chr3.fasta @ chr3:1000000 Q. of type=MIXED alleles=[A*, ATT, C] attr={BAZFIELD=BAZ, FOOFIELD=FOO} GT=[] filters=, VcfFuncotationMetadata{fieldNameToHeaderLineMap={FOOFIELD=INFO=<ID=FOOFIELD,Number=A,Type=String,Description="Description here">, BAZFIELD=INFO=<ID=BAZFIELD,Number=A,Type=String,Description="Description here">}}, TEST1) |
0s |
passed |
| testCreateFuncotations[2]([VC /tmp/funcotatorTmpFolder12282509861524526/GRCh37.p13.chr3.fasta @ chr3:1000000 Q. of type=MIXED alleles=[A*, ATT, C] attr={BAZFIELD=BAZ, FOOFIELD=FOO} GT=[] filters=, VcfFuncotationMetadata{fieldNameToHeaderLineMap={FOOFIELD=INFO=<ID=FOOFIELD,Number=A,Type=String,Description="Description here">, BAZFIELD=INFO=<ID=BAZFIELD,Number=A,Type=String,Description="Description here">, EXTRA=INFO=<ID=EXTRA,Number=A,Type=String,Description="Description here">}}, TEST1) |
0.001s |
passed |
| testCreateIntronicCDnaString[0](8, [], A, C, NA) |
0s |
passed |
| testCreateIntronicCDnaString[1](8, [testContig:20-30, testContig:40-50, testContig:60-70, testContig:80-90, testContig:10000-15000, testContig:10000000-15000000], A, T, c.e1-12A>T) |
0s |
passed |
| testCreateIntronicCDnaString[2](25, [testContig:20-30, testContig:40-50, testContig:60-70, testContig:80-90, testContig:10000-15000, testContig:10000000-15000000], C, T, c.e1+5C>T) |
0s |
passed |
| testCreateIntronicCDnaString[3](31, [testContig:20-30, testContig:40-50, testContig:60-70, testContig:80-90, testContig:10000-15000, testContig:10000000-15000000], G, T, c.e1+1G>T) |
0s |
passed |
| testCreateIntronicCDnaString[4](35, [testContig:20-30, testContig:40-50, testContig:60-70, testContig:80-90, testContig:10000-15000, testContig:10000000-15000000], ATG, GCT, c.e1+5ATG>GCT) |
0s |
passed |
| testCreateIntronicCDnaString[5](36, [testContig:20-30, testContig:40-50, testContig:60-70, testContig:80-90, testContig:10000-15000, testContig:10000000-15000000], ATG, GCT, c.e2-4ATG>GCT) |
0s |
passed |
| testCreateIntronicCDnaString[6](500, [testContig:20-30, testContig:40-50, testContig:60-70, testContig:80-90, testContig:10000-15000, testContig:10000000-15000000], TTTTTTTTT, AAAAAAAAA, c.e4+410TTTTTTTTT>AAAAAAAAA) |
0s |
passed |
| testCreateIntronicCDnaString[7](50000000, [testContig:20-30, testContig:40-50, testContig:60-70, testContig:80-90, testContig:10000-15000, testContig:10000000-15000000], A, GTG, c.e6+35000000A>GTG) |
0s |
passed |
| testCreateLinkedHashMapFromListsWithIllegalArgs[0]([K1, K2], [V1]) |
0s |
passed |
| testCreateLinkedHashMapFromListsWithIllegalArgs[1]([K1, K2], [V1, V2, V3]) |
0s |
passed |
| testCreateLinkedHashMapFromListsWithIllegalArgs[2]([K1, K2], []) |
0s |
passed |
| testCreateLinkedHashMapFromListsWithIllegalArgs[3]([K1], [V1, V2]) |
0s |
passed |
| testCreateLinkedHashMapFromListsWithIllegalArgs[4]([K1, K2, K3], [V1, V2]) |
0s |
passed |
| testCreateLinkedHashMapFromListsWithIllegalArgs[5]([], [V1, V2]) |
0.001s |
passed |
| testCreateLinkedHashMapFromListsWithIllegalArgs[6]([K1, K2, K1], [V1, V2, V3]) |
0s |
passed |
| testCreateLinkedHashMapFromListsWithIllegalArgs[7]([K1, K2, K1], [V1, V2, V1]) |
0s |
passed |
| testCreateLinkedHashMapFromLists[0]([K1, K2], [V1, V2], {K1=V1, K2=V2}) |
0s |
passed |
| testCreateLinkedHashMapFromLists[1]([C, T], [G, A], {C=G, T=A}) |
0s |
passed |
| testCreateReferenceSnippet[0](T*, C, org.broadinstitute.hellbender.engine.ReferenceContext@17ebbf1e, +, TAAGTACGTCTTCATACTCTA) |
0.001s |
passed |
| testCreateReferenceSnippet[10](CT*, TA, org.broadinstitute.hellbender.engine.ReferenceContext@62ff14cd, -, TAGAGTATGAAGACGTACTTAC) |
0s |
passed |
| testCreateReferenceSnippet[11](TCT*, ATG, org.broadinstitute.hellbender.engine.ReferenceContext@32e9c3af, -, TAGAGTATGAAGACGTACTTACC) |
0.001s |
passed |
| testCreateReferenceSnippet[12](T*, TC, org.broadinstitute.hellbender.engine.ReferenceContext@632d1b1b, -, TAGAGTATGAAGACGTACTT) |
0s |
passed |
| testCreateReferenceSnippet[13](T*, TCC, org.broadinstitute.hellbender.engine.ReferenceContext@4027edeb, -, TAGAGTATGAAGACGTACTT) |
0s |
passed |
| testCreateReferenceSnippet[14](T*, TCCA, org.broadinstitute.hellbender.engine.ReferenceContext@43b3b1b0, -, TAGAGTATGAAGACGTACTT) |
0s |
passed |
| testCreateReferenceSnippet[15](CT*, C, org.broadinstitute.hellbender.engine.ReferenceContext@7d4135c9, -, TAGAGTATGAAGACGTACTTA) |
0.001s |
passed |
| testCreateReferenceSnippet[16](TCT*, T, org.broadinstitute.hellbender.engine.ReferenceContext@4724b2c1, -, TAGAGTATGAAGACGTACTTAC) |
0s |
passed |
| testCreateReferenceSnippet[17](GTCT*, G, org.broadinstitute.hellbender.engine.ReferenceContext@193f3306, -, TAGAGTATGAAGACGTACTTACC) |
0s |
passed |
| testCreateReferenceSnippet[18](CGTCT*, C, org.broadinstitute.hellbender.engine.ReferenceContext@31aa9b01, -, TAGAGTATGAAGACGTACTTACCA) |
0s |
passed |
| testCreateReferenceSnippet[19](CT*, C, org.broadinstitute.hellbender.engine.ReferenceContext@410f1452, -, CAGGAGAGAAAGGTGAGTGGG) |
0.001s |
passed |
| testCreateReferenceSnippet[1](TT*, CC, org.broadinstitute.hellbender.engine.ReferenceContext@1f1e15de, +, TAAGTACGTCTTCATACTCTAC) |
0s |
passed |
| testCreateReferenceSnippet[2](TTC*, CGG, org.broadinstitute.hellbender.engine.ReferenceContext@1f235a0a, +, TAAGTACGTCTTCATACTCTACA) |
0s |
passed |
| testCreateReferenceSnippet[3](T*, TC, org.broadinstitute.hellbender.engine.ReferenceContext@1a0b4955, +, AAGTACGTCTTCATACTCTA) |
0s |
passed |
| testCreateReferenceSnippet[4](T*, TCC, org.broadinstitute.hellbender.engine.ReferenceContext@31434b63, +, AAGTACGTCTTCATACTCTA) |
0s |
passed |
| testCreateReferenceSnippet[5](T*, TCCA, org.broadinstitute.hellbender.engine.ReferenceContext@24558113, +, AAGTACGTCTTCATACTCTA) |
0s |
passed |
| testCreateReferenceSnippet[6](CT*, C, org.broadinstitute.hellbender.engine.ReferenceContext@166d576b, +, TAAGTACGTCTTCATACTCTA) |
0.001s |
passed |
| testCreateReferenceSnippet[7](CTT*, C, org.broadinstitute.hellbender.engine.ReferenceContext@5b407336, +, TAAGTACGTCTTCATACTCTAC) |
0s |
passed |
| testCreateReferenceSnippet[8](CTTC*, C, org.broadinstitute.hellbender.engine.ReferenceContext@6a262980, +, TAAGTACGTCTTCATACTCTACA) |
0s |
passed |
| testCreateReferenceSnippet[9](T*, C, org.broadinstitute.hellbender.engine.ReferenceContext@48a21ea6, -, TAGAGTATGAAGACGTACTTA) |
0s |
passed |
| testCreateSpliceSiteCodonChange[0](1000, 5, 1000, 1500, +, 0, c.e5-0) |
0.002s |
passed |
| testCreateSpliceSiteCodonChange[10](1000, 5, 1000, 1500, -, 4, c.e5+4) |
0s |
passed |
| testCreateSpliceSiteCodonChange[11](1000, 4, 1, 1500, -, 5, c.e4-495) |
0.001s |
passed |
| testCreateSpliceSiteCodonChange[12](1000, 3, 500, 1500, -, 6, c.e3+506) |
0s |
passed |
| testCreateSpliceSiteCodonChange[13](1000, 5, 1500, 500, -, 7, c.e5+507) |
0s |
passed |
| testCreateSpliceSiteCodonChange[14](1000, 5, 1000, 1500, +, -1, c.e5-1) |
0s |
passed |
| testCreateSpliceSiteCodonChange[15](1000, 4, 1, 1500, +, -2, c.e4+498) |
0.001s |
passed |
| testCreateSpliceSiteCodonChange[16](1000, 3, 500, 1500, +, -3, c.e3-503) |
0s |
passed |
| testCreateSpliceSiteCodonChange[17](1000, 5, 1000, 1500, -, -4, c.e5-4) |
0.001s |
passed |
| testCreateSpliceSiteCodonChange[18](1000, 4, 1, 1500, -, -5, c.e4-505) |
0s |
passed |
| testCreateSpliceSiteCodonChange[19](1000, 3, 500, 1500, -, -6, c.e3+494) |
0s |
passed |
| testCreateSpliceSiteCodonChange[1](1000, 4, 1, 1500, +, 0, c.e4+500) |
0s |
passed |
| testCreateSpliceSiteCodonChange[20](1000, 5, 1500, 500, -, -7, c.e5+493) |
0s |
passed |
| testCreateSpliceSiteCodonChange[2](1000, 3, 500, 1500, +, 0, c.e3-500) |
0s |
passed |
| testCreateSpliceSiteCodonChange[3](1000, 5, 1000, 1500, -, 0, c.e5+0) |
0s |
passed |
| testCreateSpliceSiteCodonChange[4](1000, 4, 1, 1500, -, 0, c.e4-500) |
0s |
passed |
| testCreateSpliceSiteCodonChange[5](1000, 3, 500, 1500, -, 0, c.e3+500) |
0s |
passed |
| testCreateSpliceSiteCodonChange[6](1000, 5, 1500, 500, -, 0, c.e5+500) |
0s |
passed |
| testCreateSpliceSiteCodonChange[7](1000, 5, 1000, 1500, +, 1, c.e5+1) |
0s |
passed |
| testCreateSpliceSiteCodonChange[8](1000, 4, 1, 1500, +, 2, c.e4+502) |
0s |
passed |
| testCreateSpliceSiteCodonChange[9](1000, 3, 500, 1500, +, 3, c.e3-497) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[0](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 1, 3, ATG*, 1, +, ATG) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[10](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 10, 15, GTGCCT*, 10, +, GTGCCT) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[11](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 13, 18, CCTATG*, 13, +, CCTATG) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[12](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 16, 21, ATGCTA*, 16, +, ATGCTA) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[13](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 19, 24, CTAGAT*, 19, +, CTAGAT) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[14](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 1, 69, ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG*, 1, +, ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[15](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 1, 3, CTA*, 1, -, CTA) |
0.001s |
passed |
| testGetAlignedCodingSequenceAllele[16](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 4, 6, ACA*, 4, -, ACA) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[17](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 7, 9, ACG*, 7, -, ACG) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[18](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 10, 12, CGC*, 10, -, CGC) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[19](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 13, 15, GCG*, 13, -, GCG) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[1](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 4, 6, AAA*, 4, +, AAA) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[20](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 16, 18, CGC*, 16, -, CGC) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[21](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 19, 21, GCG*, 19, -, GCG) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[22](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 1, 6, CTAACA*, 1, -, CTAACA) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[23](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 4, 9, ACAACG*, 4, -, ACAACG) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[24](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 7, 12, ACGCGC*, 7, -, ACGCGC) |
0.001s |
passed |
| testGetAlignedCodingSequenceAllele[25](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 10, 15, CGCGCG*, 10, -, CGCGCG) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[26](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 13, 18, GCGCGC*, 13, -, GCGCGC) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[27](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 16, 21, CGCGCG*, 16, -, CGCGCG) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[28](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 19, 24, GCGCAC*, 19, -, GCGCAC) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[29](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 1, 69, CTAACAACGCGCGCGCGCGCGCACACACACACACACTATCTGTCTATCTAGCATAGGCACCCCTTTCAT*, 1, -, CTAACAACGCGCGCGCGCGCGCACACACACACACACTATCTGTCTATCTAGCATAGGCACCCCTTTCAT) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[2](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 7, 9, GGG*, 7, +, GGG) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[3](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 10, 12, GTG*, 10, +, GTG) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[4](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 13, 15, CCT*, 13, +, CCT) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[5](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 16, 18, ATG*, 16, +, ATG) |
0.001s |
passed |
| testGetAlignedCodingSequenceAllele[6](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 19, 21, CTA*, 19, +, CTA) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[7](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 1, 6, ATGAAA*, 1, +, ATGAAA) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[8](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 4, 9, AAAGGG*, 4, +, AAAGGG) |
0s |
passed |
| testGetAlignedCodingSequenceAllele[9](ATGAAAGGGGTGCCTATGCTAGATAGACAGATAGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTTGTTAG, 7, 12, GGGGTG*, 7, +, GGGGTG) |
0s |
passed |
| testGetAlignedEndPositionOneArg[0](1, 3) |
0s |
passed |
| testGetAlignedEndPositionOneArg[10](11, 12) |
0s |
passed |
| testGetAlignedEndPositionOneArg[11](12, 12) |
0s |
passed |
| testGetAlignedEndPositionOneArg[1](2, 3) |
0s |
passed |
| testGetAlignedEndPositionOneArg[2](3, 3) |
0s |
passed |
| testGetAlignedEndPositionOneArg[3](4, 6) |
0.001s |
passed |
| testGetAlignedEndPositionOneArg[4](5, 6) |
0s |
passed |
| testGetAlignedEndPositionOneArg[5](6, 6) |
0s |
passed |
| testGetAlignedEndPositionOneArg[6](7, 9) |
0s |
passed |
| testGetAlignedEndPositionOneArg[7](8, 9) |
0s |
passed |
| testGetAlignedEndPositionOneArg[8](9, 9) |
0s |
passed |
| testGetAlignedEndPositionOneArg[9](10, 12) |
0s |
passed |
| testGetAlignedPosition[0](1, 1) |
0s |
passed |
| testGetAlignedPosition[10](1637, 1636) |
0s |
passed |
| testGetAlignedPosition[11](0, -2) |
0.001s |
passed |
| testGetAlignedPosition[12](-1, -2) |
0s |
passed |
| testGetAlignedPosition[13](-2, -2) |
0s |
passed |
| testGetAlignedPosition[14](-3, -5) |
0s |
passed |
| testGetAlignedPosition[15](-4, -5) |
0s |
passed |
| testGetAlignedPosition[16](-5, -5) |
0s |
passed |
| testGetAlignedPosition[1](2, 1) |
0s |
passed |
| testGetAlignedPosition[2](3, 1) |
0s |
passed |
| testGetAlignedPosition[3](4, 4) |
0s |
passed |
| testGetAlignedPosition[4](5, 4) |
0s |
passed |
| testGetAlignedPosition[5](6, 4) |
0s |
passed |
| testGetAlignedPosition[6](324, 322) |
0s |
passed |
| testGetAlignedPosition[7](325, 325) |
0s |
passed |
| testGetAlignedPosition[8](1635, 1633) |
0s |
passed |
| testGetAlignedPosition[9](1636, 1636) |
0s |
passed |
| testGetAlignedRefAllele[0](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 10, CC*, 1, -1, +, GCCCAT) |
0.001s |
passed |
| testGetAlignedRefAllele[10](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 1, AA*, 2, 1, +, AAA) |
0s |
passed |
| testGetAlignedRefAllele[11](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 2, A*, 3, 1, +, AAA) |
0s |
passed |
| testGetAlignedRefAllele[12](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 6, GGG*, 1, 1, +, GGG) |
0s |
passed |
| testGetAlignedRefAllele[13](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 7, GG*, 2, 1, +, GGG) |
0.001s |
passed |
| testGetAlignedRefAllele[14](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 8, G*, 3, 1, +, GGG) |
0s |
passed |
| testGetAlignedRefAllele[15](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 6, GGG*, 60, 60, +, GGG) |
0s |
passed |
| testGetAlignedRefAllele[16](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 7, GG*, 61, 60, +, GGG) |
0s |
passed |
| testGetAlignedRefAllele[17](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 8, G*, 62, 60, +, GGG) |
0s |
passed |
| testGetAlignedRefAllele[18](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 17, ATAG*, 18, 17, +, TATAGG) |
0s |
passed |
| testGetAlignedRefAllele[19](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 4, TTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA*, 18, 17, +, TTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA) |
0s |
passed |
| testGetAlignedRefAllele[1](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 11, CA*, 1, -1, +, CCCATG) |
0s |
passed |
| testGetAlignedRefAllele[20](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 0, TAA*, 1, 1, +, TAA) |
0s |
passed |
| testGetAlignedRefAllele[21](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 1, AG*, 2, 1, +, AAG) |
0s |
passed |
| testGetAlignedRefAllele[22](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 2, T*, 3, 1, +, AAT) |
0.001s |
passed |
| testGetAlignedRefAllele[23](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 6, GCC*, 1, 1, +, GCC) |
0s |
passed |
| testGetAlignedRefAllele[24](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 7, AG*, 2, 1, +, GAG) |
0s |
passed |
| testGetAlignedRefAllele[25](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 8, A*, 3, 1, +, GGA) |
0s |
passed |
| testGetAlignedRefAllele[26](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 6, GCC*, 60, 60, +, GCC) |
0.001s |
passed |
| testGetAlignedRefAllele[27](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 7, AG*, 61, 60, +, GAG) |
0s |
passed |
| testGetAlignedRefAllele[28](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 8, A*, 62, 60, +, GGA) |
0s |
passed |
| testGetAlignedRefAllele[29](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 17, ATAT*, 18, 17, +, TATATG) |
0s |
passed |
| testGetAlignedRefAllele[2](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 12, AT*, 1, -1, +, CCATGA) |
0s |
passed |
| testGetAlignedRefAllele[30](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 4, AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA*, 18, 17, +, TAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA) |
0s |
passed |
| testGetAlignedRefAllele[3](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 10, CC*, 0, -2, +, GCCCAT) |
0s |
passed |
| testGetAlignedRefAllele[4](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 11, CA*, 0, -2, +, CCCATG) |
0s |
passed |
| testGetAlignedRefAllele[5](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 12, AT*, 0, -2, +, CCATGA) |
0s |
passed |
| testGetAlignedRefAllele[6](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 10, CCA*, -1, -2, +, CCCATG) |
0.001s |
passed |
| testGetAlignedRefAllele[7](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 11, CAT*, -1, -2, +, CCATGA) |
0s |
passed |
| testGetAlignedRefAllele[8](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 12, ATG*, -1, -2, +, CATGAT) |
0s |
passed |
| testGetAlignedRefAllele[9](AAATTTGGGCCCATGATATAGGCGCCGTAGCAGTAGATAGCCCCCCAACCGGGGCCCGGGTTTAAA, 0, AAA*, 1, 1, +, AAA) |
0s |
passed |
| testGetAlternateSequence[0](01234567890A1234567890123456789, 12, A, A, 01234567890A1234567890123456789) |
0s |
passed |
| testGetAlternateSequence[1](01234567890A1234567890123456789, 11, A, A, 0123456789AA1234567890123456789) |
0s |
passed |
| testGetAlternateSequence[2](01234567890A1234567890123456789, 12, A, ATGCATGC, 01234567890ATGCATGC1234567890123456789) |
0.001s |
passed |
| testGetAlternateSequence[3](AAAAATTTTTGGGGGCCCCCAAAAATTTTTGGGGGCCCCC, 12, GGGGCCC, T, AAAAATTTTTGTCCAAAAATTTTTGGGGGCCCCC) |
0s |
passed |
| testGetAlternateSequence[4](A, 1, A, ATGCATGC, ATGCATGC) |
0s |
passed |
| testGetAlternateSequence[5](BA, 2, A, ATGCATGC, BATGCATGC) |
0s |
passed |
| testGetAlternateSequence[6](AB, 1, A, ATGCATGC, ATGCATGCB) |
0s |
passed |
| testGetAlternateSequence[7](ATGCATGC, 2, T, G, AGGCATGC) |
0s |
passed |
| testGetAminoAcidByLetter[0](A, Alanine) |
0s |
passed |
| testGetAminoAcidByLetter[0](A, Alanine) |
0s |
passed |
| testGetAminoAcidByLetter[10](L, Leucine) |
0.001s |
passed |
| testGetAminoAcidByLetter[10](L, Leucine) |
0s |
passed |
| testGetAminoAcidByLetter[11](K, Lysine) |
0s |
passed |
| testGetAminoAcidByLetter[11](K, Lysine) |
0s |
passed |
| testGetAminoAcidByLetter[12](M, Methionine) |
0s |
passed |
| testGetAminoAcidByLetter[12](M, Methionine) |
0s |
passed |
| testGetAminoAcidByLetter[13](F, Phenylalanine) |
0s |
passed |
| testGetAminoAcidByLetter[13](F, Phenylalanine) |
0s |
passed |
| testGetAminoAcidByLetter[14](P, Proline) |
0s |
passed |
| testGetAminoAcidByLetter[14](P, Proline) |
0s |
passed |
| testGetAminoAcidByLetter[15](S, Serine) |
0.001s |
passed |
| testGetAminoAcidByLetter[15](S, Serine) |
0.001s |
passed |
| testGetAminoAcidByLetter[16](*, Stop codon) |
0s |
passed |
| testGetAminoAcidByLetter[16](*, Stop codon) |
0s |
passed |
| testGetAminoAcidByLetter[17](T, Threonine) |
0s |
passed |
| testGetAminoAcidByLetter[17](T, Threonine) |
0s |
passed |
| testGetAminoAcidByLetter[18](W, Tryptophan) |
0s |
passed |
| testGetAminoAcidByLetter[18](W, Tryptophan) |
0s |
passed |
| testGetAminoAcidByLetter[19](Y, Tyrosine) |
0s |
passed |
| testGetAminoAcidByLetter[19](Y, Tyrosine) |
0s |
passed |
| testGetAminoAcidByLetter[1](R, Arganine) |
0s |
passed |
| testGetAminoAcidByLetter[1](R, Arganine) |
0s |
passed |
| testGetAminoAcidByLetter[20](V, Valine) |
0s |
passed |
| testGetAminoAcidByLetter[20](V, Valine) |
0s |
passed |
| testGetAminoAcidByLetter[21](a, null) |
0s |
passed |
| testGetAminoAcidByLetter[21](ahuewifaef, null) |
0.001s |
passed |
| testGetAminoAcidByLetter[22](?, null) |
0s |
passed |
| testGetAminoAcidByLetter[22](, null) |
0s |
passed |
| testGetAminoAcidByLetter[23](X, null) |
0s |
passed |
| testGetAminoAcidByLetter[23](X, null) |
0s |
passed |
| testGetAminoAcidByLetter[24](x, null) |
0s |
passed |
| testGetAminoAcidByLetter[24](x, null) |
0s |
passed |
| testGetAminoAcidByLetter[25](7, null) |
0s |
passed |
| testGetAminoAcidByLetter[25](7, null) |
0s |
passed |
| testGetAminoAcidByLetter[2](N, Asparagine) |
0s |
passed |
| testGetAminoAcidByLetter[2](N, Asparagine) |
0s |
passed |
| testGetAminoAcidByLetter[3](D, Aspartic acid) |
0s |
passed |
| testGetAminoAcidByLetter[3](D, Aspartic acid) |
0s |
passed |
| testGetAminoAcidByLetter[4](C, Cysteine) |
0s |
passed |
| testGetAminoAcidByLetter[4](C, Cysteine) |
0s |
passed |
| testGetAminoAcidByLetter[5](E, Glutamic acid) |
0s |
passed |
| testGetAminoAcidByLetter[5](E, Glutamic acid) |
0s |
passed |
| testGetAminoAcidByLetter[6](Q, Glutamine) |
0.001s |
passed |
| testGetAminoAcidByLetter[6](Q, Glutamine) |
0s |
passed |
| testGetAminoAcidByLetter[7](G, Glycine) |
0s |
passed |
| testGetAminoAcidByLetter[7](G, Glycine) |
0s |
passed |
| testGetAminoAcidByLetter[8](H, Histidine) |
0s |
passed |
| testGetAminoAcidByLetter[8](H, Histidine) |
0s |
passed |
| testGetAminoAcidByLetter[9](I, Isoleucine) |
0s |
passed |
| testGetAminoAcidByLetter[9](I, Isoleucine) |
0s |
passed |
| testGetAminoAcidCodes |
0s |
passed |
| testGetAminoAcidNames |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[0](A*, org.broadinstitute.hellbender.engine.ReferenceContext@71b32407, +, 1, TAC) |
0.001s |
passed |
| testGetBasesInWindowAroundReferenceAllele[10](ACAT*, org.broadinstitute.hellbender.engine.ReferenceContext@3c38e2bf, +, 1, TACATT) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[11](ACAT*, org.broadinstitute.hellbender.engine.ReferenceContext@3c205259, +, 2, GTACATTA) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[12](ACAT*, org.broadinstitute.hellbender.engine.ReferenceContext@20923380, +, 3, AGTACATTAA) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[13](ACAT*, org.broadinstitute.hellbender.engine.ReferenceContext@6520625f, +, 4, TAGTACATTAAC) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[14](ACAT*, org.broadinstitute.hellbender.engine.ReferenceContext@2f5a092e, +, 5, TTAGTACATTAACA) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[15](ACAT*, org.broadinstitute.hellbender.engine.ReferenceContext@70940cb8, +, 6, GTTAGTACATTAACAA) |
0.001s |
passed |
| testGetBasesInWindowAroundReferenceAllele[16](ACAT*, org.broadinstitute.hellbender.engine.ReferenceContext@7bd7c4cf, +, 7, AGTTAGTACATTAACAAT) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[17](ACAT*, org.broadinstitute.hellbender.engine.ReferenceContext@67b20b4c, +, 8, TAGTTAGTACATTAACAATG) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[18](ACAT*, org.broadinstitute.hellbender.engine.ReferenceContext@3e0a112f, +, 9, CTAGTTAGTACATTAACAATGA) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[19](ACAT*, org.broadinstitute.hellbender.engine.ReferenceContext@7da1ef46, +, 10, ACTAGTTAGTACATTAACAATGAC) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[1](A*, org.broadinstitute.hellbender.engine.ReferenceContext@400df2b3, +, 2, GTACA) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[20](T*, org.broadinstitute.hellbender.engine.ReferenceContext@1ae23815, -, 1, GTA) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[21](T*, org.broadinstitute.hellbender.engine.ReferenceContext@1165a952, -, 2, TGTAC) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[22](T*, org.broadinstitute.hellbender.engine.ReferenceContext@102f3f05, -, 3, ATGTACT) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[23](T*, org.broadinstitute.hellbender.engine.ReferenceContext@2a7b5925, -, 4, AATGTACTA) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[24](T*, org.broadinstitute.hellbender.engine.ReferenceContext@6c9b6332, -, 5, TAATGTACTAA) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[25](T*, org.broadinstitute.hellbender.engine.ReferenceContext@4889fbba, -, 6, TTAATGTACTAAC) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[26](T*, org.broadinstitute.hellbender.engine.ReferenceContext@572db5ee, -, 7, GTTAATGTACTAACT) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[27](T*, org.broadinstitute.hellbender.engine.ReferenceContext@31ab75a5, -, 8, TGTTAATGTACTAACTA) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[28](T*, org.broadinstitute.hellbender.engine.ReferenceContext@2dec57c5, -, 9, TTGTTAATGTACTAACTAG) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[29](T*, org.broadinstitute.hellbender.engine.ReferenceContext@31e9d94f, -, 10, ATTGTTAATGTACTAACTAGT) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[2](A*, org.broadinstitute.hellbender.engine.ReferenceContext@18ffc008, +, 3, AGTACAT) |
0.001s |
passed |
| testGetBasesInWindowAroundReferenceAllele[30](TGTA*, org.broadinstitute.hellbender.engine.ReferenceContext@4987142d, -, 1, AATGTA) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[31](TGTA*, org.broadinstitute.hellbender.engine.ReferenceContext@41e76252, -, 2, TAATGTAC) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[32](TGTA*, org.broadinstitute.hellbender.engine.ReferenceContext@67376bae, -, 3, TTAATGTACT) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[33](TGTA*, org.broadinstitute.hellbender.engine.ReferenceContext@7c59cf66, -, 4, GTTAATGTACTA) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[34](TGTA*, org.broadinstitute.hellbender.engine.ReferenceContext@37816ea6, -, 5, TGTTAATGTACTAA) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[35](TGTA*, org.broadinstitute.hellbender.engine.ReferenceContext@35b79b1f, -, 6, TTGTTAATGTACTAAC) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[36](TGTA*, org.broadinstitute.hellbender.engine.ReferenceContext@5a8835c6, -, 7, ATTGTTAATGTACTAACT) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[37](TGTA*, org.broadinstitute.hellbender.engine.ReferenceContext@6ec77cab, -, 8, CATTGTTAATGTACTAACTA) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[38](TGTA*, org.broadinstitute.hellbender.engine.ReferenceContext@17c72ffa, -, 9, TCATTGTTAATGTACTAACTAG) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[39](TGTA*, org.broadinstitute.hellbender.engine.ReferenceContext@2e1c8027, -, 10, GTCATTGTTAATGTACTAACTAGT) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[3](A*, org.broadinstitute.hellbender.engine.ReferenceContext@694f0655, +, 4, TAGTACATT) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[4](A*, org.broadinstitute.hellbender.engine.ReferenceContext@5d08a65c, +, 5, TTAGTACATTA) |
0.001s |
passed |
| testGetBasesInWindowAroundReferenceAllele[5](A*, org.broadinstitute.hellbender.engine.ReferenceContext@4d7f9b33, +, 6, GTTAGTACATTAA) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[6](A*, org.broadinstitute.hellbender.engine.ReferenceContext@608c7b5b, +, 7, AGTTAGTACATTAAC) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[7](A*, org.broadinstitute.hellbender.engine.ReferenceContext@17d45cfb, +, 8, TAGTTAGTACATTAACA) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[8](A*, org.broadinstitute.hellbender.engine.ReferenceContext@1c65ec63, +, 9, CTAGTTAGTACATTAACAA) |
0s |
passed |
| testGetBasesInWindowAroundReferenceAllele[9](A*, org.broadinstitute.hellbender.engine.ReferenceContext@10f192d8, +, 10, ACTAGTTAGTACATTAACAAT) |
0s |
passed |
| testGetClosestExonIndex[0](8, [], -1) |
0s |
passed |
| testGetClosestExonIndex[1](8, [testContig:20-30, testContig:40-50, testContig:60-70, testContig:80-90, testContig:10000-15000, testContig:10000000-15000000], 0) |
0s |
passed |
| testGetClosestExonIndex[2](25, [testContig:20-30, testContig:40-50, testContig:60-70, testContig:80-90, testContig:10000-15000, testContig:10000000-15000000], 0) |
0s |
passed |
| testGetClosestExonIndex[3](31, [testContig:20-30, testContig:40-50, testContig:60-70, testContig:80-90, testContig:10000-15000, testContig:10000000-15000000], 0) |
0s |
passed |
| testGetClosestExonIndex[4](35, [testContig:20-30, testContig:40-50, testContig:60-70, testContig:80-90, testContig:10000-15000, testContig:10000000-15000000], 0) |
0.002s |
passed |
| testGetClosestExonIndex[5](36, [testContig:20-30, testContig:40-50, testContig:60-70, testContig:80-90, testContig:10000-15000, testContig:10000000-15000000], 1) |
0s |
passed |
| testGetClosestExonIndex[6](500, [testContig:20-30, testContig:40-50, testContig:60-70, testContig:80-90, testContig:10000-15000, testContig:10000000-15000000], 3) |
0s |
passed |
| testGetClosestExonIndex[7](50000000, [testContig:20-30, testContig:40-50, testContig:60-70, testContig:80-90, testContig:10000-15000, testContig:10000000-15000000], 5) |
0s |
passed |
| testGetCodingSequenceChangeString[0](1632, A, T, +, c.1632A>T) |
0s |
passed |
| testGetCodingSequenceChangeString[1](1633, CT, GG, +, c.1633_1634CT>GG) |
0s |
passed |
| testGetCodingSequenceChangeString[2](1634, T, TGG, +, c.1634_1635insGG) |
0s |
passed |
| testGetCodingSequenceChangeString[3](43303, A, TCA, -, c.43302_43303insTC) |
0s |
passed |
| testGetCodingSequenceChangeString[4](1634, TGAG, T, +, c.1635_1637delGAG) |
0s |
passed |
| testGetCodingSequenceChangeString[5](43138, TCT, T, -, c.43138_43139delTC) |
0s |
passed |
| testGetCodonChangeString[0](G, T, 178921515, 997, 997, GCA, TCA, TCA, 999, chr3, +, ReferenceSequence ENST00000263967.3|ENSG00000121879.3|OTTHUMG00000157311.2|OTTHUMT00000348409.2|PIK3CA-001|PIK3CA|9093|UTR5:1-157|CDS:158-3364|UTR3:3365-9093|, chr3:178916614-178916616, c.(997-999)Gca>Tca) |
0s |
passed |
| testGetCodonChangeString[10](TGCA, T, 178921514, 996, 994, AGTGCA, AGT, AGT, 996, chr3, +, ReferenceSequence ENST00000263967.3|ENSG00000121879.3|OTTHUMG00000157311.2|OTTHUMT00000348409.2|PIK3CA-001|PIK3CA|9093|UTR5:1-157|CDS:158-3364|UTR3:3365-9093|, chr3:178916614-178916616, c.(997-999)gcadel) |
0.001s |
passed |
| testGetCodonChangeString[11](TCCT, T, 9091794, 21, 19, CTTCCT, CTT, CTT, 21, chr19, -, ReferenceSequence ENST00000397910.4|ENSG00000181143.11|OTTHUMG00000169191.3|OTTHUMT00000402806.1|MUC16-001|MUC16|43816|UTR5:1-204|CDS:205-43728|UTR3:43729-43816|, chr19:9091812-9091814, c.(19-24)cttcct>ctt) |
0s |
passed |
| testGetCodonChangeString[12](GCAC, G, 178921515, 997, 997, GCACTC, GTC, GTC, 999, chr3, +, ReferenceSequence ENST00000263967.3|ENSG00000121879.3|OTTHUMG00000157311.2|OTTHUMT00000348409.2|PIK3CA-001|PIK3CA|9093|UTR5:1-157|CDS:158-3364|UTR3:3365-9093|, chr3:178916614-178916616, c.(997-1002)gcactc>gtc) |
0s |
passed |
| testGetCodonChangeString[1](C, T, 178921516, 998, 997, GCA, GTA, GTA, 999, chr3, +, ReferenceSequence ENST00000263967.3|ENSG00000121879.3|OTTHUMG00000157311.2|OTTHUMT00000348409.2|PIK3CA-001|PIK3CA|9093|UTR5:1-157|CDS:158-3364|UTR3:3365-9093|, chr3:178916614-178916616, c.(997-999)gCa>gTa) |
0s |
passed |
| testGetCodonChangeString[2](A, T, 178921517, 999, 997, GCA, GCT, GCT, 999, chr3, +, ReferenceSequence ENST00000263967.3|ENSG00000121879.3|OTTHUMG00000157311.2|OTTHUMT00000348409.2|PIK3CA-001|PIK3CA|9093|UTR5:1-157|CDS:158-3364|UTR3:3365-9093|, chr3:178916614-178916616, c.(997-999)gcA>gcT) |
0s |
passed |
| testGetCodonChangeString[3](A, AT, 178916614, 1, 1, ATG, ATTG, ATTG, 3, chr3, +, ReferenceSequence ENST00000263967.3|ENSG00000121879.3|OTTHUMG00000157311.2|OTTHUMT00000348409.2|PIK3CA-001|PIK3CA|9093|UTR5:1-157|CDS:158-3364|UTR3:3365-9093|, chr3:178916614-178916616, ) |
0s |
passed |
| testGetCodonChangeString[4](G, GC, 178921515, 997, 997, GCA, GCCA, GCCA, 999, chr3, +, ReferenceSequence ENST00000263967.3|ENSG00000121879.3|OTTHUMG00000157311.2|OTTHUMT00000348409.2|PIK3CA-001|PIK3CA|9093|UTR5:1-157|CDS:158-3364|UTR3:3365-9093|, chr3:178916614-178916616, c.(997-999)gcafs) |
0s |
passed |
| testGetCodonChangeString[5](A, TGTA, 9091814, 1, 1, ATG, TGTATG, TGTATG, 3, chr19, -, ReferenceSequence ENST00000397910.4|ENSG00000181143.11|OTTHUMG00000169191.3|OTTHUMT00000402806.1|MUC16-001|MUC16|43816|UTR5:1-204|CDS:205-43728|UTR3:43729-43816|, chr19:9091812-9091814, c.(1-3)atg>TGTatg) |
0s |
passed |
| testGetCodonChangeString[6](A, AGCG, 178921515, 999, 997, GCA, GCAGCG, GCAGCG, 999, chr3, +, ReferenceSequence ENST00000263967.3|ENSG00000121879.3|OTTHUMG00000157311.2|OTTHUMT00000348409.2|PIK3CA-001|PIK3CA|9093|UTR5:1-157|CDS:158-3364|UTR3:3365-9093|, chr3:178916614-178916616, c.(1000-1002)ctc>GCGctc) |
0s |
passed |
| testGetCodonChangeString[7](T, TTCG, 9091794, 21, 19, CTT, CTCGTT, CTCGTT, 21, chr19, -, ReferenceSequence ENST00000397910.4|ENSG00000181143.11|OTTHUMG00000169191.3|OTTHUMT00000402806.1|MUC16-001|MUC16|43816|UTR5:1-204|CDS:205-43728|UTR3:43729-43816|, chr19:9091812-9091814, c.(19-21)ctt>ctCGTt) |
0s |
passed |
| testGetCodonChangeString[8](G, GCAG, 178921515, 997, 997, GCA, GCAGCA, GCAGCA, 999, chr3, +, ReferenceSequence ENST00000263967.3|ENSG00000121879.3|OTTHUMG00000157311.2|OTTHUMT00000348409.2|PIK3CA-001|PIK3CA|9093|UTR5:1-157|CDS:158-3364|UTR3:3365-9093|, chr3:178916614-178916616, c.(997-999)gca>gCAGca) |
0s |
passed |
| testGetCodonChangeString[9](C, CG, 9091793, 22, 22, CCT, CGCT, CGCT, 24, chr19, -, ReferenceSequence ENST00000397910.4|ENSG00000181143.11|OTTHUMG00000169191.3|OTTHUMT00000402806.1|MUC16-001|MUC16|43816|UTR5:1-204|CDS:205-43728|UTR3:43729-43816|, chr19:9091812-9091814, c.(22-24)cctfs) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[0](null, null) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[10](AGR, Arganine) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[11](CGY, Arganine) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[12](MGR, Arganine) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[13](AAY, Asparagine) |
0.001s |
passed |
| testGetEukaryoticAminoAcidByCodon[14](GAY, Aspartic acid) |
0.001s |
passed |
| testGetEukaryoticAminoAcidByCodon[15](TGY, Cysteine) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[16](CAR, Glutamine) |
0.001s |
passed |
| testGetEukaryoticAminoAcidByCodon[17](GAR, Glutamic acid) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[18](GGN, Glycine) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[19](CAY, Histidine) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[1](, null) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[20](ATH, Isoleucine) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[21](CTN, Leucine) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[22](TTR, Leucine) |
0.001s |
passed |
| testGetEukaryoticAminoAcidByCodon[23](CTY, Leucine) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[24](YTR, Leucine) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[25](AAR, Lysine) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[26](TTY, Phenylalanine) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[27](CCN, Proline) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[28](TCN, Serine) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[29](AGY, Serine) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[2](XQZ, null) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[30](ACN, Threonine) |
0.001s |
passed |
| testGetEukaryoticAminoAcidByCodon[31](TAY, Tyrosine) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[32](GTN, Valine) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[33](TRA, Stop codon) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[34](TAR, Stop codon) |
0.001s |
passed |
| testGetEukaryoticAminoAcidByCodon[3](ATG, Methionine) |
0.001s |
passed |
| testGetEukaryoticAminoAcidByCodon[4](CCA, Proline) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[5](CCC, Proline) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[6](CCG, Proline) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[7](CCT, Proline) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[8](GCN, Alanine) |
0s |
passed |
| testGetEukaryoticAminoAcidByCodon[9](CGN, Arganine) |
0s |
passed |
| testGetIndelAdjustedAlleleChangeStartPosition[0]([VC null @ 1:1 Q. of type=SNP alleles=[A*, T] attr={} GT=[] filters=, 1) |
0s |
passed |
| testGetIndelAdjustedAlleleChangeStartPosition[1]([VC null @ 1:1 Q. of type=INDEL alleles=[A*, TG] attr={} GT=[] filters=, 1) |
0s |
passed |
| testGetIndelAdjustedAlleleChangeStartPosition[2]([VC null @ 1:1234 Q. of type=INDEL alleles=[A*, AT] attr={} GT=[] filters=, 1235) |
0s |
passed |
| testGetIndelAdjustedAlleleChangeStartPosition[3]([VC null @ 1:1234 Q. of type=INDEL alleles=[A*, ATG] attr={} GT=[] filters=, 1235) |
0s |
passed |
| testGetIndelAdjustedAlleleChangeStartPosition[4]([VC null @ 1:1234 Q. of type=INDEL alleles=[A*, ATGTC] attr={} GT=[] filters=, 1235) |
0s |
passed |
| testGetIndelAdjustedAlleleChangeStartPosition[5]([VC null @ 1:1234-1236 Q. of type=INDEL alleles=[ATG*, AT] attr={} GT=[] filters=, 1236) |
0.001s |
passed |
| testGetIndelAdjustedAlleleChangeStartPosition[6]([VC null @ 1:1234-1236 Q. of type=INDEL alleles=[ATG*, A] attr={} GT=[] filters=, 1235) |
0s |
passed |
| testGetIndelAdjustedAlleleChangeStartPosition[7]([VC null @ 1:1234-1237 Q. of type=INDEL alleles=[ATGT*, ATGTC] attr={} GT=[] filters=, 1238) |
0s |
passed |
| testGetIndelAdjustedAlleleChangeStartPosition[8]([VC null @ 1:1234-1238 Q. of type=INDEL alleles=[ATGTC*, ATGT] attr={} GT=[] filters=, 1238) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[0](null, false, UNSPECIFIED, null) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[10](CCT, false, UNSPECIFIED, Proline) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[11](ATT, false, UNSPECIFIED, Isoleucine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[12](ATA, false, UNSPECIFIED, Methionine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[13](AGA, false, UNSPECIFIED, Stop codon) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[14](AGG, false, UNSPECIFIED, Stop codon) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[15](TGA, false, UNSPECIFIED, Tryptophan) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[16](ATA, true, BOS, Methionine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[17](ATA, true, HOMO, Methionine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[18](ATT, true, HOMO, Methionine) |
0.001s |
passed |
| testGetMitochondrialAminoAcidByCodon[19](ATT, true, MUS, Methionine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[1](, false, UNSPECIFIED, null) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[20](ATC, true, MUS, Methionine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[21](ATY, true, MUS, Methionine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[22](GTG, true, CORTURNIX, Methionine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[23](GTG, true, GALLUS, Methionine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[24](GCN, false, UNSPECIFIED, Alanine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[25](CGN, false, UNSPECIFIED, Arganine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[26](CGY, false, UNSPECIFIED, Arganine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[27](MGR, false, UNSPECIFIED, Arganine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[28](AAY, false, UNSPECIFIED, Asparagine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[29](GAY, false, UNSPECIFIED, Aspartic acid) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[2](XQZ, false, UNSPECIFIED, null) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[30](TGY, false, UNSPECIFIED, Cysteine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[31](CAR, false, UNSPECIFIED, Glutamine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[32](GAR, false, UNSPECIFIED, Glutamic acid) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[33](GGN, false, UNSPECIFIED, Glycine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[34](CAY, false, UNSPECIFIED, Histidine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[35](ATH, false, UNSPECIFIED, Isoleucine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[36](CTN, false, UNSPECIFIED, Leucine) |
0.001s |
passed |
| testGetMitochondrialAminoAcidByCodon[37](TTR, false, UNSPECIFIED, Leucine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[38](CTY, false, UNSPECIFIED, Leucine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[39](YTR, false, UNSPECIFIED, Leucine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[3](null, false, UNSPECIFIED, null) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[40](AAR, false, UNSPECIFIED, Lysine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[41](TTY, false, UNSPECIFIED, Phenylalanine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[42](CCN, false, UNSPECIFIED, Proline) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[43](TCN, false, UNSPECIFIED, Serine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[44](AGY, false, UNSPECIFIED, Serine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[45](ACN, false, UNSPECIFIED, Threonine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[46](TAY, false, UNSPECIFIED, Tyrosine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[47](GTN, false, UNSPECIFIED, Valine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[48](TRA, false, UNSPECIFIED, Stop codon) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[49](TAR, false, UNSPECIFIED, Stop codon) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[4](, false, UNSPECIFIED, null) |
0.001s |
passed |
| testGetMitochondrialAminoAcidByCodon[50](AGR, false, UNSPECIFIED, Stop codon) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[5](XQZ, false, UNSPECIFIED, null) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[6](ATG, false, UNSPECIFIED, Methionine) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[7](CCA, false, UNSPECIFIED, Proline) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[8](CCC, false, UNSPECIFIED, Proline) |
0s |
passed |
| testGetMitochondrialAminoAcidByCodon[9](CCG, false, UNSPECIFIED, Proline) |
0s |
passed |
| testGetNonOverlappingAltAlleleBaseString[0](A*, A, false, ) |
0s |
passed |
| testGetNonOverlappingAltAlleleBaseString[10](AAAAAAAAAA*, TAAAA, false, T) |
0s |
passed |
| testGetNonOverlappingAltAlleleBaseString[11](AAAAAAAAAA*, AAAAT, false, T) |
0s |
passed |
| testGetNonOverlappingAltAlleleBaseString[12](AAAAAAAAAA*, ATTTT, false, TTTT) |
0s |
passed |
| testGetNonOverlappingAltAlleleBaseString[13](AAAAAAAAAA*, TTTTA, false, TTTT) |
0s |
passed |
| testGetNonOverlappingAltAlleleBaseString[1](AAAAAAAAAA*, AAAAAAAAAA, false, ) |
0s |
passed |
| testGetNonOverlappingAltAlleleBaseString[2](AAAAAAAAAA*, TAAAAAAAAA, false, T) |
0.004s |
passed |
| testGetNonOverlappingAltAlleleBaseString[3](AAAAAAAAAA*, AAAAAAAAAT, false, T) |
0s |
passed |
| testGetNonOverlappingAltAlleleBaseString[4](AAAAAAAAAA*, ATTTTTTTTT, false, TTTTTTTTT) |
0s |
passed |
| testGetNonOverlappingAltAlleleBaseString[5](AAAAAAAAAA*, TTTTTTTTTA, false, TTTTTTTTT) |
0s |
passed |
| testGetNonOverlappingAltAlleleBaseString[6](AAAAA*, TAAAAAAAAA, false, TAAAA) |
0s |
passed |
| testGetNonOverlappingAltAlleleBaseString[7](AAAAA*, AAAAAAAAAT, false, AAAAT) |
0.001s |
passed |
| testGetNonOverlappingAltAlleleBaseString[8](AAAAA*, ATTTTTTTTT, false, TTTTTTTTT) |
0s |
passed |
| testGetNonOverlappingAltAlleleBaseString[9](AAAAA*, TTTTTTTTTA, false, TTTTTTTTT) |
0s |
passed |
| testGetOverlappingExonPositions[0](A*, T, chr3, 50, 50, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], null) |
0s |
passed |
| testGetOverlappingExonPositions[10](ATGCATGCAT*, GCATGCATGC, chr3, 120, 129, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:100-199) |
0s |
passed |
| testGetOverlappingExonPositions[11](ATGCATGCAT*, GCATGCATGC, chr3, 199, 208, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:100-199) |
0s |
passed |
| testGetOverlappingExonPositions[12](A*, T, chr3, 300, 300, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:300-399) |
0s |
passed |
| testGetOverlappingExonPositions[13](A*, T, chr3, 350, 350, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:300-399) |
0.001s |
passed |
| testGetOverlappingExonPositions[14](A*, T, chr3, 399, 399, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:300-399) |
0.001s |
passed |
| testGetOverlappingExonPositions[15](ATGCATGCAT*, GCATGCATGC, chr3, 291, 300, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:300-399) |
0s |
passed |
| testGetOverlappingExonPositions[16](ATGCATGCAT*, GCATGCATGC, chr3, 320, 329, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:300-399) |
0s |
passed |
| testGetOverlappingExonPositions[17](ATGCATGCAT*, GCATGCATGC, chr3, 399, 408, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:300-399) |
0s |
passed |
| testGetOverlappingExonPositions[18](A*, T, chr3, 500, 500, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:500-599) |
0s |
passed |
| testGetOverlappingExonPositions[19](A*, T, chr3, 550, 550, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:500-599) |
0s |
passed |
| testGetOverlappingExonPositions[1](A*, T, chr3, 299, 299, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], null) |
0s |
passed |
| testGetOverlappingExonPositions[20](A*, T, chr3, 599, 599, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:500-599) |
0s |
passed |
| testGetOverlappingExonPositions[21](ATGCATGCAT*, GCATGCATGC, chr3, 491, 500, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:500-599) |
0s |
passed |
| testGetOverlappingExonPositions[22](ATGCATGCAT*, GCATGCATGC, chr3, 520, 529, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:500-599) |
0s |
passed |
| testGetOverlappingExonPositions[23](ATGCATGCAT*, GCATGCATGC, chr3, 599, 608, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:500-599) |
0s |
passed |
| testGetOverlappingExonPositions[24](A*, T, chr3, 700, 700, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:700-799) |
0s |
passed |
| testGetOverlappingExonPositions[25](A*, T, chr3, 750, 750, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:700-799) |
0s |
passed |
| testGetOverlappingExonPositions[26](A*, T, chr3, 799, 799, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:700-799) |
0s |
passed |
| testGetOverlappingExonPositions[27](ATGCATGCAT*, GCATGCATGC, chr3, 691, 700, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:700-799) |
0s |
passed |
| testGetOverlappingExonPositions[28](ATGCATGCAT*, GCATGCATGC, chr3, 720, 729, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:700-799) |
0s |
passed |
| testGetOverlappingExonPositions[29](ATGCATGCAT*, GCATGCATGC, chr3, 799, 808, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:700-799) |
0s |
passed |
| testGetOverlappingExonPositions[2](A*, T, chr3, 400, 400, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], null) |
0s |
passed |
| testGetOverlappingExonPositions[30](A*, T, chr3, 900, 900, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:900-999) |
0s |
passed |
| testGetOverlappingExonPositions[31](A*, T, chr3, 950, 950, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:900-999) |
0s |
passed |
| testGetOverlappingExonPositions[32](A*, T, chr3, 999, 999, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:900-999) |
0.001s |
passed |
| testGetOverlappingExonPositions[33](ATGCATGCAT*, GCATGCATGC, chr3, 891, 900, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:900-999) |
0s |
passed |
| testGetOverlappingExonPositions[34](ATGCATGCAT*, GCATGCATGC, chr3, 920, 929, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:900-999) |
0s |
passed |
| testGetOverlappingExonPositions[35](ATGCATGCAT*, GCATGCATGC, chr3, 999, 1008, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:900-999) |
0s |
passed |
| testGetOverlappingExonPositions[36](A*, T, chr3, 50, 50, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], null) |
0s |
passed |
| testGetOverlappingExonPositions[37](A*, T, chr3, 299, 299, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], null) |
0s |
passed |
| testGetOverlappingExonPositions[38](A*, T, chr3, 400, 400, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], null) |
0.001s |
passed |
| testGetOverlappingExonPositions[39](ATGCATGCAT*, GCATGCATGC, chr3, 40, 49, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], null) |
0s |
passed |
| testGetOverlappingExonPositions[3](ATGCATGCAT*, GCATGCATGC, chr3, 40, 49, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], null) |
0s |
passed |
| testGetOverlappingExonPositions[40](ATGCATGCAT*, GCATGCATGC, chr3, 290, 299, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], null) |
0s |
passed |
| testGetOverlappingExonPositions[41](ATGCATGCAT*, GCATGCATGC, chr3, 400, 409, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], null) |
0s |
passed |
| testGetOverlappingExonPositions[42](A*, T, chr3, 100, 100, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:100-199) |
0s |
passed |
| testGetOverlappingExonPositions[43](A*, T, chr3, 150, 150, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:100-199) |
0s |
passed |
| testGetOverlappingExonPositions[44](A*, T, chr3, 199, 199, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:100-199) |
0s |
passed |
| testGetOverlappingExonPositions[45](ATGCATGCAT*, GCATGCATGC, chr3, 91, 100, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:100-199) |
0.001s |
passed |
| testGetOverlappingExonPositions[46](ATGCATGCAT*, GCATGCATGC, chr3, 120, 129, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:100-199) |
0s |
passed |
| testGetOverlappingExonPositions[47](ATGCATGCAT*, GCATGCATGC, chr3, 199, 208, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:100-199) |
0s |
passed |
| testGetOverlappingExonPositions[48](A*, T, chr3, 300, 300, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:300-399) |
0s |
passed |
| testGetOverlappingExonPositions[49](A*, T, chr3, 350, 350, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:300-399) |
0s |
passed |
| testGetOverlappingExonPositions[4](ATGCATGCAT*, GCATGCATGC, chr3, 290, 299, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], null) |
0.001s |
passed |
| testGetOverlappingExonPositions[50](A*, T, chr3, 399, 399, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:300-399) |
0s |
passed |
| testGetOverlappingExonPositions[51](ATGCATGCAT*, GCATGCATGC, chr3, 291, 300, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:300-399) |
0s |
passed |
| testGetOverlappingExonPositions[52](ATGCATGCAT*, GCATGCATGC, chr3, 320, 329, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:300-399) |
0s |
passed |
| testGetOverlappingExonPositions[53](ATGCATGCAT*, GCATGCATGC, chr3, 399, 408, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:300-399) |
0.001s |
passed |
| testGetOverlappingExonPositions[54](A*, T, chr3, 500, 500, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:500-599) |
0s |
passed |
| testGetOverlappingExonPositions[55](A*, T, chr3, 550, 550, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:500-599) |
0s |
passed |
| testGetOverlappingExonPositions[56](A*, T, chr3, 599, 599, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:500-599) |
0s |
passed |
| testGetOverlappingExonPositions[57](ATGCATGCAT*, GCATGCATGC, chr3, 491, 500, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:500-599) |
0s |
passed |
| testGetOverlappingExonPositions[58](ATGCATGCAT*, GCATGCATGC, chr3, 520, 529, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:500-599) |
0s |
passed |
| testGetOverlappingExonPositions[59](ATGCATGCAT*, GCATGCATGC, chr3, 599, 608, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:500-599) |
0s |
passed |
| testGetOverlappingExonPositions[5](ATGCATGCAT*, GCATGCATGC, chr3, 400, 409, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], null) |
0s |
passed |
| testGetOverlappingExonPositions[60](A*, T, chr3, 700, 700, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:700-799) |
0s |
passed |
| testGetOverlappingExonPositions[61](A*, T, chr3, 750, 750, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:700-799) |
0s |
passed |
| testGetOverlappingExonPositions[62](A*, T, chr3, 799, 799, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:700-799) |
0s |
passed |
| testGetOverlappingExonPositions[63](ATGCATGCAT*, GCATGCATGC, chr3, 691, 700, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:700-799) |
0s |
passed |
| testGetOverlappingExonPositions[64](ATGCATGCAT*, GCATGCATGC, chr3, 720, 729, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:700-799) |
0s |
passed |
| testGetOverlappingExonPositions[65](ATGCATGCAT*, GCATGCATGC, chr3, 799, 808, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:700-799) |
0s |
passed |
| testGetOverlappingExonPositions[66](A*, T, chr3, 900, 900, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:900-999) |
0s |
passed |
| testGetOverlappingExonPositions[67](A*, T, chr3, 950, 950, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:900-999) |
0.001s |
passed |
| testGetOverlappingExonPositions[68](A*, T, chr3, 999, 999, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:900-999) |
0s |
passed |
| testGetOverlappingExonPositions[69](ATGCATGCAT*, GCATGCATGC, chr3, 891, 900, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:900-999) |
0s |
passed |
| testGetOverlappingExonPositions[6](A*, T, chr3, 100, 100, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:100-199) |
0s |
passed |
| testGetOverlappingExonPositions[70](ATGCATGCAT*, GCATGCATGC, chr3, 920, 929, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:900-999) |
0s |
passed |
| testGetOverlappingExonPositions[71](ATGCATGCAT*, GCATGCATGC, chr3, 999, 1008, -, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:900-999) |
0s |
passed |
| testGetOverlappingExonPositions[7](A*, T, chr3, 150, 150, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:100-199) |
0s |
passed |
| testGetOverlappingExonPositions[8](A*, T, chr3, 199, 199, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:100-199) |
0s |
passed |
| testGetOverlappingExonPositions[9](ATGCATGCAT*, GCATGCATGC, chr3, 91, 100, +, [chr3:100-199, chr3:300-399, chr3:500-599, chr3:700-799, chr3:900-999], chr3:100-199) |
0s |
passed |
| testGetProteinChangeEndPosition[0](1, 3, 1) |
0s |
passed |
| testGetProteinChangeEndPosition[1](1, 6, 2) |
0s |
passed |
| testGetProteinChangeEndPosition[2](1, 9, 3) |
0s |
passed |
| testGetProteinChangeEndPosition[3](1, 12, 4) |
0s |
passed |
| testGetProteinChangeEndPosition[4](1, 15, 5) |
0s |
passed |
| testGetProteinChangeEndPosition[5](1, 18, 6) |
0s |
passed |
| testGetProteinChangeEndPosition[6](1, 21, 7) |
0s |
passed |
| testGetProteinChangeEndPosition[7](1, 24, 8) |
0s |
passed |
| testGetProteinChangePosition[0](1, 1) |
0s |
passed |
| testGetProteinChangePosition[10](304, 102) |
0s |
passed |
| testGetProteinChangePosition[1](2, 1) |
0s |
passed |
| testGetProteinChangePosition[2](3, 1) |
0s |
passed |
| testGetProteinChangePosition[3](4, 2) |
0s |
passed |
| testGetProteinChangePosition[4](5, 2) |
0s |
passed |
| testGetProteinChangePosition[5](6, 2) |
0s |
passed |
| testGetProteinChangePosition[6](300, 100) |
0s |
passed |
| testGetProteinChangePosition[7](301, 101) |
0s |
passed |
| testGetProteinChangePosition[8](302, 101) |
0s |
passed |
| testGetProteinChangePosition[9](303, 101) |
0s |
passed |
| testGetStartPositionInTranscript[0](chr1:1-1, [chr1:10-19, chr1:30-39, chr1:50-59, chr1:70-79, chr1:90-99], +, -1) |
0s |
passed |
| testGetStartPositionInTranscript[10](chr1:105-392, [chr1:90-99, chr1:70-79, chr1:50-59, chr1:30-39, chr1:10-19], -, -1) |
0s |
passed |
| testGetStartPositionInTranscript[11](chr1:10-10, [chr1:90-99, chr1:70-79, chr1:50-59, chr1:30-39, chr1:10-19], -, 50) |
0s |
passed |
| testGetStartPositionInTranscript[12](chr1:99-99, [chr1:90-99, chr1:70-79, chr1:50-59, chr1:30-39, chr1:10-19], -, 1) |
0s |
passed |
| testGetStartPositionInTranscript[13](chr1:50-67, [chr1:90-99, chr1:70-79, chr1:50-59, chr1:30-39, chr1:10-19], -, -1) |
0s |
passed |
| testGetStartPositionInTranscript[14](chr1:67-75, [chr1:90-99, chr1:70-79, chr1:50-59, chr1:30-39, chr1:10-19], -, 15) |
0s |
passed |
| testGetStartPositionInTranscript[15](3:178936090-178936096, [3:178916614-178916965, 3:178917478-178917687, 3:178919078-178919328, 3:178921332-178921577, 3:178922291-178922376, 3:178927383-178927488, 3:178927974-178928126, 3:178928219-178928353, 3:178935998-178936122], +, 1632) |
0s |
passed |
| testGetStartPositionInTranscript[1](chr1:25-67, [chr1:10-19, chr1:30-39, chr1:50-59, chr1:70-79, chr1:90-99], +, -1) |
0s |
passed |
| testGetStartPositionInTranscript[2](chr1:105-392, [chr1:10-19, chr1:30-39, chr1:50-59, chr1:70-79, chr1:90-99], +, -1) |
0s |
passed |
| testGetStartPositionInTranscript[3](chr1:10-10, [chr1:10-19, chr1:30-39, chr1:50-59, chr1:70-79, chr1:90-99], +, 1) |
0.001s |
passed |
| testGetStartPositionInTranscript[4](chr1:99-99, [chr1:10-19, chr1:30-39, chr1:50-59, chr1:70-79, chr1:90-99], +, 50) |
0s |
passed |
| testGetStartPositionInTranscript[5](chr1:50-67, [chr1:10-19, chr1:30-39, chr1:50-59, chr1:70-79, chr1:90-99], +, 21) |
0s |
passed |
| testGetStartPositionInTranscript[6](chr1:67-75, [chr1:10-19, chr1:30-39, chr1:50-59, chr1:70-79, chr1:90-99], +, -1) |
0.001s |
passed |
| testGetStartPositionInTranscript[7](chr1:91-97, [chr1:10-19, chr1:30-39, chr1:50-59, chr1:70-79, chr1:90-99], +, 42) |
0s |
passed |
| testGetStartPositionInTranscript[8](chr1:1-1, [chr1:90-99, chr1:70-79, chr1:50-59, chr1:30-39, chr1:10-19], -, -1) |
0s |
passed |
| testGetStartPositionInTranscript[9](chr1:25-67, [chr1:90-99, chr1:70-79, chr1:50-59, chr1:30-39, chr1:10-19], -, -1) |
0s |
passed |
| testGetStrandCorrectedAllele[0](A, +, A) |
0s |
passed |
| testGetStrandCorrectedAllele[10](AATT, -, AATT) |
0s |
passed |
| testGetStrandCorrectedAllele[11](AATTG, -, CAATT) |
0s |
passed |
| testGetStrandCorrectedAllele[12](AATTGC, -, GCAATT) |
0s |
passed |
| testGetStrandCorrectedAllele[13](AATTGCG, -, CGCAATT) |
0s |
passed |
| testGetStrandCorrectedAllele[1](AA, +, AA) |
0s |
passed |
| testGetStrandCorrectedAllele[2](AAT, +, AAT) |
0s |
passed |
| testGetStrandCorrectedAllele[3](AATT, +, AATT) |
0s |
passed |
| testGetStrandCorrectedAllele[4](AATTG, +, AATTG) |
0s |
passed |
| testGetStrandCorrectedAllele[5](AATTGC, +, AATTGC) |
0.001s |
passed |
| testGetStrandCorrectedAllele[6](AATTGCG, +, AATTGCG) |
0s |
passed |
| testGetStrandCorrectedAllele[7](A, -, T) |
0s |
passed |
| testGetStrandCorrectedAllele[8](AA, -, TT) |
0s |
passed |
| testGetStrandCorrectedAllele[9](AAT, -, ATT) |
0s |
passed |
| testGetTranscriptAlleleStartPosition[0]([VC @ 1:100 Q. of type=SNP alleles=[A*, T] attr={} GT=[] filters=, [1:100-100], +, 1) |
0.001s |
passed |
| testGetTranscriptAlleleStartPosition[1]([VC @ 1:100 Q. of type=SNP alleles=[A*, T] attr={} GT=[] filters=, [1:100-100], -, 1) |
0s |
passed |
| testGetTranscriptAlleleStartPosition[2]([VC @ 1:100 Q. of type=SNP alleles=[A*, T] attr={} GT=[] filters=, [1:50-200], +, 51) |
0s |
passed |
| testGetTranscriptAlleleStartPosition[3]([VC @ 1:100 Q. of type=SNP alleles=[A*, T] attr={} GT=[] filters=, [1:50-200], -, 101) |
0s |
passed |
| testGetTranscriptAlleleStartPosition[4]([VC @ 1:100 Q. of type=SNP alleles=[A*, T] attr={} GT=[] filters=, [1:50-100, 1:101-200], +, 51) |
0s |
passed |
| testGetTranscriptAlleleStartPosition[5]([VC @ 1:100 Q. of type=SNP alleles=[A*, T] attr={} GT=[] filters=, [1:50-100, 1:101-200], -, 101) |
0s |
passed |
| testGetTranscriptAlleleStartPosition[6]([VC @ 1:100 Q. of type=SNP alleles=[A*, T] attr={} GT=[] filters=, [1:1-10, 1:11-20, 1:21-30, 1:31-40, 1:41-50, 1:51-60, 1:61-70, 1:71-80, 1:81-90, 1:91-100, 1:101-110, 1:111-120, 1:121-130, 1:131-140, 1:141-150, 1:151-160, 1:161-170, 1:171-180, 1:181-190, 1:191-200], +, 100) |
0.001s |
passed |
| testGetTranscriptAlleleStartPosition[7]([VC @ 1:100 Q. of type=SNP alleles=[A*, T] attr={} GT=[] filters=, [1:1-10, 1:11-20, 1:21-30, 1:31-40, 1:41-50, 1:51-60, 1:61-70, 1:71-80, 1:81-90, 1:91-100, 1:101-110, 1:111-120, 1:121-130, 1:131-140, 1:141-150, 1:151-160, 1:161-170, 1:171-180, 1:181-190, 1:191-200], -, 101) |
0s |
passed |
| testIsGencodeFuncotation[0](TableFuncotation{dataSourceName='TEST', fieldMap={FIELD:VALUE}, altAllele=A}, false) |
0s |
passed |
| testIsGencodeFuncotation[1](org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@86509ba7, true) |
0s |
passed |
| testIsInFrameWithEndOfRegion[0](1, 1, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[10](1, 10, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[11](2, 10, true) |
0s |
passed |
| testIsInFrameWithEndOfRegion[12](3, 10, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[13](4, 10, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[14](5, 10, true) |
0s |
passed |
| testIsInFrameWithEndOfRegion[15](6, 10, false) |
0.002s |
passed |
| testIsInFrameWithEndOfRegion[16](7, 10, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[17](8, 10, true) |
0s |
passed |
| testIsInFrameWithEndOfRegion[18](9, 10, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[19](10, 10, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[1](1, 2, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[20](56, 473, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[21](57, 473, true) |
0s |
passed |
| testIsInFrameWithEndOfRegion[22](58, 473, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[23](10, 10, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[24](11, 11, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[25](12, 12, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[26](100, 100, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[27](1000, 1000, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[28](1, 1, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[29](0, 1, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[2](1, 3, true) |
0s |
passed |
| testIsInFrameWithEndOfRegion[30](-1, 1, true) |
0s |
passed |
| testIsInFrameWithEndOfRegion[31](-2, 1, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[32](-3, 1, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[33](-4, 1, true) |
0s |
passed |
| testIsInFrameWithEndOfRegion[34](1, 2, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[35](0, 2, true) |
0s |
passed |
| testIsInFrameWithEndOfRegion[36](-1, 2, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[37](-2, 2, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[38](-3, 2, true) |
0s |
passed |
| testIsInFrameWithEndOfRegion[39](-4, 2, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[3](1, 4, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[4](1, 5, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[5](1, 6, true) |
0s |
passed |
| testIsInFrameWithEndOfRegion[6](1, 7, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[7](1, 8, false) |
0s |
passed |
| testIsInFrameWithEndOfRegion[8](1, 9, true) |
0s |
passed |
| testIsInFrameWithEndOfRegion[9](1, 10, false) |
0s |
passed |
| testIsIndelBetweenCodons[0](4, 4, A, +, false) |
0s |
passed |
| testIsIndelBetweenCodons[10](5, 4, A, -, false) |
0s |
passed |
| testIsIndelBetweenCodons[11](6, 4, A, -, false) |
0s |
passed |
| testIsIndelBetweenCodons[12](4, 4, AC, -, true) |
0s |
passed |
| testIsIndelBetweenCodons[13](5, 4, AC, -, false) |
0s |
passed |
| testIsIndelBetweenCodons[14](6, 4, AC, -, false) |
0s |
passed |
| testIsIndelBetweenCodons[15](4, 4, ACT, -, true) |
0.001s |
passed |
| testIsIndelBetweenCodons[16](5, 4, ACT, -, false) |
0s |
passed |
| testIsIndelBetweenCodons[17](6, 4, ACT, -, false) |
0s |
passed |
| testIsIndelBetweenCodons[1](5, 4, A, +, false) |
0s |
passed |
| testIsIndelBetweenCodons[2](6, 4, A, +, true) |
0s |
passed |
| testIsIndelBetweenCodons[3](4, 4, AC, +, false) |
0s |
passed |
| testIsIndelBetweenCodons[4](5, 4, AC, +, true) |
0s |
passed |
| testIsIndelBetweenCodons[5](6, 4, AC, +, false) |
0s |
passed |
| testIsIndelBetweenCodons[6](4, 4, ACT, +, true) |
0s |
passed |
| testIsIndelBetweenCodons[7](5, 4, ACT, +, false) |
0s |
passed |
| testIsIndelBetweenCodons[8](6, 4, ACT, +, false) |
0s |
passed |
| testIsIndelBetweenCodons[9](4, 4, A, -, true) |
0s |
passed |
| testIsPositionInFrame[0](1, true) |
0s |
passed |
| testIsPositionInFrame[10](289, true) |
0s |
passed |
| testIsPositionInFrame[11](290, false) |
0s |
passed |
| testIsPositionInFrame[12](291, false) |
0s |
passed |
| testIsPositionInFrame[13](292, true) |
0s |
passed |
| testIsPositionInFrame[14](293, false) |
0s |
passed |
| testIsPositionInFrame[15](294, false) |
0.001s |
passed |
| testIsPositionInFrame[1](2, false) |
0s |
passed |
| testIsPositionInFrame[2](3, false) |
0s |
passed |
| testIsPositionInFrame[3](4, true) |
0s |
passed |
| testIsPositionInFrame[4](5, false) |
0s |
passed |
| testIsPositionInFrame[5](6, false) |
0s |
passed |
| testIsPositionInFrame[6](7, true) |
0s |
passed |
| testIsPositionInFrame[7](8, false) |
0s |
passed |
| testIsPositionInFrame[8](9, false) |
0s |
passed |
| testIsPositionInFrame[9](10, true) |
0s |
passed |
| testRenderProteinChangeString[0](1, 1, N, N, C, A, TEST:1-3, 1, p.N1N) |
0.001s |
passed |
| testRenderProteinChangeString[10](5, 5, V, I, TT, CG, TEST:1-3, 1, p.V5I) |
0s |
passed |
| testRenderProteinChangeString[11](10, 10, R, *, AA, GT, TEST:1-3, 1, p.R10*) |
0s |
passed |
| testRenderProteinChangeString[12](100, 100, *, L, AG, TC, TEST:1-3, 1, p.*100L) |
0s |
passed |
| testRenderProteinChangeString[13](1, 2, NK, TG, CG, AT, null, 1, p.1_2NK>TG) |
0s |
passed |
| testRenderProteinChangeString[14](1, 2, NK, TG, CG, AT, TEST:1-3, 1, p.1_2NK>TG) |
0s |
passed |
| testRenderProteinChangeString[15](5, 6, FV, LI, TT, CG, TEST:1-3, 1, p.5_6FV>LI) |
0.002s |
passed |
| testRenderProteinChangeString[16](10, 11, RS, W*, AA, GT, TEST:1-3, 1, p.10_11RS>W*) |
0s |
passed |
| testRenderProteinChangeString[17](100, 101, Q*, FL, AG, TC, TEST:1-3, 1, p.100_101Q*>FL) |
0s |
passed |
| testRenderProteinChangeString[18](2, 2, R, R, CGA, AGG, null, 1, p.R2R) |
0s |
passed |
| testRenderProteinChangeString[19](1, 1, I, G, ATT, GGA, null, 1, p.I1G) |
0s |
passed |
| testRenderProteinChangeString[1](1, 1, N, K, C, A, null, 1, p.N1K) |
0s |
passed |
| testRenderProteinChangeString[20](5, 5, V, T, GTT, ACC, TEST:1-3, 1, p.V5T) |
0s |
passed |
| testRenderProteinChangeString[21](101, 102, LS, FR, ATC, TCG, null, 1, p.101_102LS>FR) |
0s |
passed |
| testRenderProteinChangeString[22](201, 202, VK, GR, TGA, GGC, TEST:1-3, 1, p.201_202VK>GR) |
0s |
passed |
| testRenderProteinChangeString[23](2, 5, RQV*, RQV*, CGCCAGGTGTAA, CGTCAAGTTTGA, null, 1, p.2_5RQV*>RQV*) |
0s |
passed |
| testRenderProteinChangeString[24](10, 32, RACDEFGHIKLMNPQRSTVWYR, RACDEFGHIKLMNPQRSTVWYR, CGCGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCGTGTGGTATCGC, AGAGCTTGTGACGAGTTCGGACACATCAAGTTCATGAATCCCCAAAGAAGAACAGTATGGTACAGA, TEST:1-3, 1, p.10_32RACDEFGHIKLMNPQRSTVWYR>RACDEFGHIKLMNPQRSTVWYR) |
0s |
passed |
| testRenderProteinChangeString[25](17, 18, F*, LT, CTAG, GACT, null, 1, p.17_18F*>LT) |
0s |
passed |
| testRenderProteinChangeString[26](51, 60, ACDEFGHIKL, MNPQRSTVWY, GCGTGCGATGAATTTGGCCATATTAAACTG, ATGAACCCGCAGCGCAGCACCGTGTGGTAT, null, 1, p.51_60ACDEFGHIKL>MNPQRSTVWY) |
0s |
passed |
| testRenderProteinChangeString[27](1, 1, M, M, A, ATG, TEST:1-3, 1, ) |
0s |
passed |
| testRenderProteinChangeString[28](1, 1, M, M, A, AT, TEST:1-3, 1, ) |
0s |
passed |
| testRenderProteinChangeString[29](1, 1, M, M, T, TG, TEST:1-3, 2, ) |
0s |
passed |
| testRenderProteinChangeString[2](1, 1, N, K, C, A, TEST:1-3, 1, p.N1K) |
0s |
passed |
| testRenderProteinChangeString[30](1, 1, M, M, T, TGC, TEST:1-3, 2, ) |
0s |
passed |
| testRenderProteinChangeString[31](2, 2, K, K, T, TG, TEST:1-3, 3, p.K2fs) |
0s |
passed |
| testRenderProteinChangeString[32](4, 4, G, G, C, CA, TEST:1-3, 10, p.G4fs) |
0s |
passed |
| testRenderProteinChangeString[33](4, 4, G, G, C, CAC, TEST:1-3, 10, p.G4fs) |
0s |
passed |
| testRenderProteinChangeString[34](4, 4, Q, Q, A, ATG, TEST:1-3, 10, p.Q4fs) |
0s |
passed |
| testRenderProteinChangeString[35](4, 4, V, V, T, TG, TEST:1-3, 10, p.V4fs) |
0s |
passed |
| testRenderProteinChangeString[36](1, 1, M, M, ATG, AT, TEST:1-3, 1, ) |
0s |
passed |
| testRenderProteinChangeString[37](1, 1, M, M, AT, A, TEST:1-3, 1, ) |
0s |
passed |
| testRenderProteinChangeString[38](1, 1, M, M, TG, T, TEST:1-3, 2, ) |
0s |
passed |
| testRenderProteinChangeString[39](1, 1, M, M, CA, C, TEST:100-102, 99, ) |
0s |
passed |
| testRenderProteinChangeString[3](5, 5, F, L, C, A, TEST:1-3, 1, p.F5L) |
0s |
passed |
| testRenderProteinChangeString[40](4, 4, M, M, ATG, AT, TEST:1-3, 10, p.M4fs) |
0s |
passed |
| testRenderProteinChangeString[41](5, 5, V, V, AT, A, TEST:1-3, 12, p.V5fs) |
0s |
passed |
| testRenderProteinChangeString[42](10, 10, W, W, TG, T, TEST:1-3, 30, p.W10fs) |
0s |
passed |
| testRenderProteinChangeString[43](9, 9, GS, GS, CTGGG, C, TEST:1-3, 27, p.GS9fs) |
0s |
passed |
| testRenderProteinChangeString[44](544, 545, , G, T, TGGA, TEST:1-3, 178936090, p.544_545insG) |
0s |
passed |
| testRenderProteinChangeString[45](545, 546, , W, G, GTGG, TEST:1-3, 178936093, p.545_546insW) |
0s |
passed |
| testRenderProteinChangeString[46](544, 545, , GC, T, TGGACTT, TEST:1-3, 178936090, p.544_545insGC) |
0s |
passed |
| testRenderProteinChangeString[47](545, 546, , W*, G, GTGGTGA, TEST:1-3, 178936093, p.545_546insW*) |
0s |
passed |
| testRenderProteinChangeString[48](544, 545, , GCA, T, TGGACTTATT, TEST:1-3, 178936090, p.544_545insGCA) |
0s |
passed |
| testRenderProteinChangeString[49](545, 546, , WV*, G, GTGGGTATGA, TEST:1-3, 178936093, p.545_546insWV*) |
0s |
passed |
| testRenderProteinChangeString[4](10, 10, A, V, C, G, TEST:1-3, 1, p.A10V) |
0s |
passed |
| testRenderProteinChangeString[50](544, 545, , A, A, ACTG, TEST:1-3, 178936088, p.544_545insA) |
0s |
passed |
| testRenderProteinChangeString[51](544, 545, , S, C, CCAG, TEST:1-3, 178936089, p.544_545insS) |
0s |
passed |
| testRenderProteinChangeString[52](544, 545, T, IA, A, ATCG, TEST:1-3, 178936088, p.544_545T>IA) |
0s |
passed |
| testRenderProteinChangeString[53](545, 545, E, DV*, G, GATGTCT, TEST:1-3, 178936091, p.E545DV*) |
0s |
passed |
| testRenderProteinChangeString[54](545, 545, E, DLQ, A, ACCTGCA, TEST:1-3, 178936092, p.E545DLQ) |
0s |
passed |
| testRenderProteinChangeString[55](545, 546, , QE, A, AGCAGGA, TEST:1-3, 178936092, p.545_546insQE) |
0s |
passed |
| testRenderProteinChangeString[56](544, 544, T, , CACT, C, TEST:1-3, 1631, p.T544del) |
0s |
passed |
| testRenderProteinChangeString[57](545, 545, E, , TGAG, T, TEST:1-3, 1634, p.E545del) |
0s |
passed |
| testRenderProteinChangeString[58](544, 544, TE, , CACTGAG, C, TEST:1-3, 1631, p.TE544del) |
0s |
passed |
| testRenderProteinChangeString[59](545, 545, EQ, , TGAGCAG, T, TEST:1-3, 1634, p.EQ545del) |
0s |
passed |
| testRenderProteinChangeString[5](100, 100, Y, P, A, T, TEST:1-3, 1, p.Y100P) |
0s |
passed |
| testRenderProteinChangeString[60](544, 544, TEQ, , CACTGAGCAG, C, TEST:1-3, 1631, p.TEQ544del) |
0s |
passed |
| testRenderProteinChangeString[61](545, 545, EQE, , TGAGCAGGAG, T, TEST:1-3, 1634, p.EQE545del) |
0s |
passed |
| testRenderProteinChangeString[62](544, 545, TE, K, ACTG, A, TEST:1-3, 1632, p.544_545TE>K) |
0s |
passed |
| testRenderProteinChangeString[63](545, 545, E, E, CTGA, C, TEST:1-3, 1633, p.E545del) |
0s |
passed |
| testRenderProteinChangeString[64](544, 546, TEQ, K, ACTGAGC, A, TEST:1-3, 1632, p.544_546TEQ>K) |
0.001s |
passed |
| testRenderProteinChangeString[65](545, 545, EQ, , CTGAGCA, C, TEST:1-3, 1633, p.EQ545del) |
0s |
passed |
| testRenderProteinChangeString[66](545, 545, EQE, , ACTGAGCAGG, A, TEST:1-3, 1632, p.EQE545del) |
0s |
passed |
| testRenderProteinChangeString[67](545, 545, EQE, , CTGAGCAGGA, C, TEST:1-3, 1633, p.EQE545del) |
0s |
passed |
| testRenderProteinChangeString[6](2, 2, K, K, CG, AT, null, 1, p.K2K) |
0s |
passed |
| testRenderProteinChangeString[7](1, 2, NK, NK, CG, AT, null, 1, p.1_2NK>NK) |
0s |
passed |
| testRenderProteinChangeString[8](1, 1, N, G, CG, AT, null, 1, p.N1G) |
0s |
passed |
| testRenderProteinChangeString[9](1, 1, K, T, CG, AT, TEST:1-3, 1, p.K1T) |
0s |
passed |
| testRenderSanitizedFuncotationForVcf[0](TableFuncotation{dataSourceName='FAKEDATA', fieldMap={FOO:BAR , BAZ:HUH?}, altAllele=T}, [FOO, BAZ], BAR|HUH?) |
0s |
passed |
| testRenderSanitizedFuncotationForVcf[1](TableFuncotation{dataSourceName='FAKEDATA', fieldMap={FOO:BAR , BAZ:HUH?}, altAllele=T}, [FOO], BAR) |
0.001s |
passed |
| testRenderSanitizedFuncotationForVcf[2](TableFuncotation{dataSourceName='FAKEDATA', fieldMap={FOO:BAR , BAZ:HUH?}, altAllele=T}, [FOO, NOTHERE], BAR) |
0s |
passed |
| testRenderSanitizedFuncotationForVcf[3](TableFuncotation{dataSourceName='FAKEDATA', fieldMap={FOO:BAR , BAZ:HUH?}, altAllele=T}, [FOO, BAZ, NOTHERE], BAR|HUH?) |
0s |
passed |
| testSanitizeFuncotationFieldForMaf[0]( HAHAHAH , _%09_HAHAHAH_%09_) |
0s |
passed |
| testSanitizeFuncotationFieldForMaf[1]( HAHAHAH
, _%09_HAHAHAH_%0A_) |
0s |
passed |
| testSanitizeFuncotationFieldForMaf[2](FOO, FOO) |
0s |
passed |
| testSanitizeFuncotationFieldForVcf[0](, ) |
0s |
passed |
| testSanitizeFuncotationFieldForVcf[10](ASDFJKL:, ASDFJKL:) |
0s |
passed |
| testSanitizeFuncotationFieldForVcf[11](ASDF;JKL:, ASDF_%3B_JKL:) |
0s |
passed |
| testSanitizeFuncotationFieldForVcf[1](,, _%2C_) |
0s |
passed |
| testSanitizeFuncotationFieldForVcf[2](;, _%3B_) |
0s |
passed |
| testSanitizeFuncotationFieldForVcf[3](=, _%3D_) |
0s |
passed |
| testSanitizeFuncotationFieldForVcf[4]( , _%09_) |
0s |
passed |
| testSanitizeFuncotationFieldForVcf[5](|, _%7C_) |
0s |
passed |
| testSanitizeFuncotationFieldForVcf[6]( , _%20_) |
0s |
passed |
| testSanitizeFuncotationFieldForVcf[7](
, _%0A_) |
0s |
passed |
| testSanitizeFuncotationFieldForVcf[8](#, _%23_) |
0s |
passed |
| testSanitizeFuncotationFieldForVcf[9](,;= |
#, _%2C__%3B__%3D__%09__%7C__%20__%0A__%23_) |
0s |
passed |
| testSetVariantClassificationCustomSeverityBadVcName |
0.001s |
passed |
| testSetVariantClassificationCustomSeverityNonIntSev |
0.001s |
passed |
| testSetVariantClassificationCustomSeverityNonexistentFile |
0.001s |
passed |
| testSetVariantClassificationCustomSeverityWrongColumnsTsv |
0.003s |
passed |
| testSetVariantClassificationCustomSeverity[0](/gatkCloneMountPoint/src/test/resources/large/funcotator/custom_vc_order_files/test1.tsv, {INTRON=1, FIVE_PRIME_FLANK=16, NONSTOP=256, THREE_PRIME_FLANK=32, IN_FRAME_INS=4096, COULD_NOT_DETERMINE=0, SILENT=512, START_CODON_SNP=32768, SPLICE_SITE=1024, FRAME_SHIFT_DEL=16384, LINCRNA=2097152, NONSENSE=128, FIVE_PRIME_UTR=2, DE_NOVO_START_IN_FRAME=262144, RNA=1048576, THREE_PRIME_UTR=4, START_CODON_DEL=131072, MISSENSE=64, START_CODON_INS=65536, IN_FRAME_DEL=2048, FRAME_SHIFT_INS=8192, DE_NOVO_START_OUT_FRAME=524288, IGR=8}) |
0s |
passed |
| testSetVariantClassificationCustomSeverity[1](/gatkCloneMountPoint/src/test/resources/large/funcotator/custom_vc_order_files/test2.tsv, {INTRON=1, FIVE_PRIME_FLANK=15, NONSTOP=0, THREE_PRIME_FLANK=16, IN_FRAME_INS=4096, COULD_NOT_DETERMINE=0, SILENT=5, START_CODON_SNP=3, SPLICE_SITE=1024, LINCRNA=2097152, FRAME_SHIFT_DEL=2, NONSENSE=0, FIVE_PRIME_UTR=2, DE_NOVO_START_IN_FRAME=1, RNA=1048576, THREE_PRIME_UTR=4, START_CODON_DEL=3, MISSENSE=1, START_CODON_INS=3, IN_FRAME_DEL=2048, FRAME_SHIFT_INS=2, DE_NOVO_START_OUT_FRAME=0, IGR=8}) |
0s |
passed |
| testSetVariantClassificationCustomSeverity[2](/gatkCloneMountPoint/src/test/resources/large/funcotator/custom_vc_order_files/test3.tsv, {INTRON=10, FIVE_PRIME_FLANK=15, NONSTOP=0, THREE_PRIME_FLANK=16, IN_FRAME_INS=1, COULD_NOT_DETERMINE=99, SILENT=5, START_CODON_SNP=3, LINCRNA=2097152, SPLICE_SITE=4, FRAME_SHIFT_DEL=2, NONSENSE=0, FIVE_PRIME_UTR=6, DE_NOVO_START_IN_FRAME=1, RNA=4, THREE_PRIME_UTR=6, START_CODON_DEL=3, MISSENSE=1, START_CODON_INS=3, IN_FRAME_DEL=1, FRAME_SHIFT_INS=2, DE_NOVO_START_OUT_FRAME=0, IGR=20}) |
0.001s |
passed |