| Test |
Duration |
Result |
| testCacheOnObjectReference |
0.814s |
passed |
| testCreateFuncotationMetadata[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/dbSNP_hg19_snippet.vcf, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:61650 Q. of type=SNP alleles=[T*, C] attr={} GT=[] filters=, org.broadinstitute.hellbender.engine.ReferenceContext@74d6d5ca, [TableFuncotation{dataSourceName='TestFactory', fieldMap={TestFactory_ASP:false , TestFactory_ASS:false , TestFactory_CAF: , TestFactory_CDA:false , TestFactory_CFL:false , TestFactory_COMMON: , TestFactory_DSS:false , TestFactory_G5:false , TestFactory_G5A:false , TestFactory_GENEINFO: , TestFactory_GNO:false , TestFactory_HD:false , TestFactory_INT:false , TestFactory_KGPhase1:false , TestFactory_KGPhase3:false , TestFactory_LSD:false , TestFactory_MTP:false , TestFactory_MUT:false , TestFactory_NOC:false , TestFactory_NOV:false , TestFactory_NSF:false , TestFactory_NSM:false , TestFactory_NSN:false , TestFactory_OM:false , TestFactory_OTH:false , TestFactory_PM:false , TestFactory_PMC:false , TestFactory_R3:false , TestFactory_R5:false , TestFactory_REF:false , TestFactory_RS: , TestFactory_RSPOS: , TestFactory_RV:false , TestFactory_S3D:false , TestFactory_SAO: , TestFactory_SLO:false , TestFactory_SSR: , TestFactory_SYN:false , TestFactory_TOPMED: , TestFactory_TPA:false , TestFactory_U3:false , TestFactory_U5:false , TestFactory_VC: , TestFactory_VLD:false , TestFactory_VP: , TestFactory_WGT: , TestFactory_WTD:false , TestFactory_dbSNPBuildID: , TestFactory_ID: , TestFactory_FILTER:}, altAllele=C}]) |
0.009s |
passed |
| testCreateFuncotationMetadata[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/dbSNP_hg19_snippet.vcf, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:61662 Q. of type=SNP alleles=[T*, C] attr={} GT=[] filters=, org.broadinstitute.hellbender.engine.ReferenceContext@74239871, [TableFuncotation{dataSourceName='TestFactory', fieldMap={TestFactory_ASP:true , TestFactory_ASS:false , TestFactory_CAF:0.9744,0.02556 , TestFactory_CDA:false , TestFactory_CFL:false , TestFactory_COMMON:1 , TestFactory_DSS:false , TestFactory_G5:true , TestFactory_G5A:false , TestFactory_GENEINFO: , TestFactory_GNO:false , TestFactory_HD:true , TestFactory_INT:false , TestFactory_KGPhase1:true , TestFactory_KGPhase3:true , TestFactory_LSD:false , TestFactory_MTP:false , TestFactory_MUT:false , TestFactory_NOC:false , TestFactory_NOV:false , TestFactory_NSF:false , TestFactory_NSM:false , TestFactory_NSN:false , TestFactory_OM:false , TestFactory_OTH:false , TestFactory_PM:false , TestFactory_PMC:false , TestFactory_R3:false , TestFactory_R5:false , TestFactory_REF:false , TestFactory_RS:73009205 , TestFactory_RSPOS:61662 , TestFactory_RV:false , TestFactory_S3D:false , TestFactory_SAO:0 , TestFactory_SLO:true , TestFactory_SSR:0 , TestFactory_SYN:false , TestFactory_TOPMED:0.954392,0.0456075 , TestFactory_TPA:false , TestFactory_U3:false , TestFactory_U5:false , TestFactory_VC:SNV , TestFactory_VLD:true , TestFactory_VP:0x05010000000515043e000100 , TestFactory_WGT:1 , TestFactory_WTD:false , TestFactory_dbSNPBuildID:130 , TestFactory_ID:rs73009205 , TestFactory_FILTER:}, altAllele=C}]) |
0.007s |
passed |
| testCreateFuncotationMetadata[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/dbSNP_hg19_snippet.vcf, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:64157-64166 Q. of type=MNP alleles=[AGAAAGGTCA*, TCTTTCCAGT] attr={} GT=[] filters=, org.broadinstitute.hellbender.engine.ReferenceContext@294c1b45, [TableFuncotation{dataSourceName='TestFactory', fieldMap={TestFactory_ASP:false , TestFactory_ASS:false , TestFactory_CAF: , TestFactory_CDA:false , TestFactory_CFL:false , TestFactory_COMMON: , TestFactory_DSS:false , TestFactory_G5:false , TestFactory_G5A:false , TestFactory_GENEINFO: , TestFactory_GNO:false , TestFactory_HD:false , TestFactory_INT:false , TestFactory_KGPhase1:false , TestFactory_KGPhase3:false , TestFactory_LSD:false , TestFactory_MTP:false , TestFactory_MUT:false , TestFactory_NOC:false , TestFactory_NOV:false , TestFactory_NSF:false , TestFactory_NSM:false , TestFactory_NSN:false , TestFactory_OM:false , TestFactory_OTH:false , TestFactory_PM:false , TestFactory_PMC:false , TestFactory_R3:false , TestFactory_R5:false , TestFactory_REF:false , TestFactory_RS: , TestFactory_RSPOS: , TestFactory_RV:false , TestFactory_S3D:false , TestFactory_SAO: , TestFactory_SLO:false , TestFactory_SSR: , TestFactory_SYN:false , TestFactory_TOPMED: , TestFactory_TPA:false , TestFactory_U3:false , TestFactory_U5:false , TestFactory_VC: , TestFactory_VLD:false , TestFactory_VP: , TestFactory_WGT: , TestFactory_WTD:false , TestFactory_dbSNPBuildID: , TestFactory_ID: , TestFactory_FILTER:}, altAllele=TCTTTCCAGT}]) |
0.010s |
passed |
| testCreateFuncotationMetadata[3](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/dbSNP_hg19_snippet_with_filters.vcf, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:61662 Q. of type=SNP alleles=[T*, C] attr={} GT=[] filters=, org.broadinstitute.hellbender.engine.ReferenceContext@5bc3c4e5, [TableFuncotation{dataSourceName='TestFactory', fieldMap={TestFactory_ASP:true , TestFactory_ASS:false , TestFactory_CAF:0.9744,0.02556 , TestFactory_CDA:false , TestFactory_CFL:false , TestFactory_COMMON:1 , TestFactory_DSS:false , TestFactory_G5:true , TestFactory_G5A:false , TestFactory_GENEINFO: , TestFactory_GNO:false , TestFactory_HD:true , TestFactory_INT:false , TestFactory_KGPhase1:true , TestFactory_KGPhase3:true , TestFactory_LSD:false , TestFactory_MTP:false , TestFactory_MUT:false , TestFactory_NOC:false , TestFactory_NOV:false , TestFactory_NSF:false , TestFactory_NSM:false , TestFactory_NSN:false , TestFactory_OM:false , TestFactory_OTH:false , TestFactory_PM:false , TestFactory_PMC:false , TestFactory_R3:false , TestFactory_R5:false , TestFactory_REF:false , TestFactory_RS:73009205 , TestFactory_RSPOS:61662 , TestFactory_RV:false , TestFactory_S3D:false , TestFactory_SAO:0 , TestFactory_SLO:true , TestFactory_SSR:0 , TestFactory_SYN:false , TestFactory_TOPMED:0.954392,0.0456075 , TestFactory_TPA:false , TestFactory_U3:false , TestFactory_U5:false , TestFactory_VC:SNV , TestFactory_VLD:true , TestFactory_VP:0x05010000000515043e000100 , TestFactory_WGT:1 , TestFactory_WTD:false , TestFactory_dbSNPBuildID:130 , TestFactory_ID:rs73009205 , TestFactory_FILTER:FILTER_73}, altAllele=C}]) |
0.011s |
passed |
| testCreateFuncotationsOnVariant[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/dbSNP_hg19_snippet.vcf, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:61650 Q. of type=SNP alleles=[T*, C] attr={} GT=[] filters=, org.broadinstitute.hellbender.engine.ReferenceContext@61cf810c, [TableFuncotation{dataSourceName='TestFactory', fieldMap={TestFactory_ASP:false , TestFactory_ASS:false , TestFactory_CAF: , TestFactory_CDA:false , TestFactory_CFL:false , TestFactory_COMMON: , TestFactory_DSS:false , TestFactory_G5:false , TestFactory_G5A:false , TestFactory_GENEINFO: , TestFactory_GNO:false , TestFactory_HD:false , TestFactory_INT:false , TestFactory_KGPhase1:false , TestFactory_KGPhase3:false , TestFactory_LSD:false , TestFactory_MTP:false , TestFactory_MUT:false , TestFactory_NOC:false , TestFactory_NOV:false , TestFactory_NSF:false , TestFactory_NSM:false , TestFactory_NSN:false , TestFactory_OM:false , TestFactory_OTH:false , TestFactory_PM:false , TestFactory_PMC:false , TestFactory_R3:false , TestFactory_R5:false , TestFactory_REF:false , TestFactory_RS: , TestFactory_RSPOS: , TestFactory_RV:false , TestFactory_S3D:false , TestFactory_SAO: , TestFactory_SLO:false , TestFactory_SSR: , TestFactory_SYN:false , TestFactory_TOPMED: , TestFactory_TPA:false , TestFactory_U3:false , TestFactory_U5:false , TestFactory_VC: , TestFactory_VLD:false , TestFactory_VP: , TestFactory_WGT: , TestFactory_WTD:false , TestFactory_dbSNPBuildID: , TestFactory_ID: , TestFactory_FILTER:}, altAllele=C}]) |
0.003s |
passed |
| testCreateFuncotationsOnVariant[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/dbSNP_hg19_snippet.vcf, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:61662 Q. of type=SNP alleles=[T*, C] attr={} GT=[] filters=, org.broadinstitute.hellbender.engine.ReferenceContext@2bd2fa2c, [TableFuncotation{dataSourceName='TestFactory', fieldMap={TestFactory_ASP:true , TestFactory_ASS:false , TestFactory_CAF:0.9744,0.02556 , TestFactory_CDA:false , TestFactory_CFL:false , TestFactory_COMMON:1 , TestFactory_DSS:false , TestFactory_G5:true , TestFactory_G5A:false , TestFactory_GENEINFO: , TestFactory_GNO:false , TestFactory_HD:true , TestFactory_INT:false , TestFactory_KGPhase1:true , TestFactory_KGPhase3:true , TestFactory_LSD:false , TestFactory_MTP:false , TestFactory_MUT:false , TestFactory_NOC:false , TestFactory_NOV:false , TestFactory_NSF:false , TestFactory_NSM:false , TestFactory_NSN:false , TestFactory_OM:false , TestFactory_OTH:false , TestFactory_PM:false , TestFactory_PMC:false , TestFactory_R3:false , TestFactory_R5:false , TestFactory_REF:false , TestFactory_RS:73009205 , TestFactory_RSPOS:61662 , TestFactory_RV:false , TestFactory_S3D:false , TestFactory_SAO:0 , TestFactory_SLO:true , TestFactory_SSR:0 , TestFactory_SYN:false , TestFactory_TOPMED:0.954392,0.0456075 , TestFactory_TPA:false , TestFactory_U3:false , TestFactory_U5:false , TestFactory_VC:SNV , TestFactory_VLD:true , TestFactory_VP:0x05010000000515043e000100 , TestFactory_WGT:1 , TestFactory_WTD:false , TestFactory_dbSNPBuildID:130 , TestFactory_ID:rs73009205 , TestFactory_FILTER:}, altAllele=C}]) |
0.003s |
passed |
| testCreateFuncotationsOnVariant[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/dbSNP_hg19_snippet.vcf, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:64157-64166 Q. of type=MNP alleles=[AGAAAGGTCA*, TCTTTCCAGT] attr={} GT=[] filters=, org.broadinstitute.hellbender.engine.ReferenceContext@7e2cebdf, [TableFuncotation{dataSourceName='TestFactory', fieldMap={TestFactory_ASP:false , TestFactory_ASS:false , TestFactory_CAF: , TestFactory_CDA:false , TestFactory_CFL:false , TestFactory_COMMON: , TestFactory_DSS:false , TestFactory_G5:false , TestFactory_G5A:false , TestFactory_GENEINFO: , TestFactory_GNO:false , TestFactory_HD:false , TestFactory_INT:false , TestFactory_KGPhase1:false , TestFactory_KGPhase3:false , TestFactory_LSD:false , TestFactory_MTP:false , TestFactory_MUT:false , TestFactory_NOC:false , TestFactory_NOV:false , TestFactory_NSF:false , TestFactory_NSM:false , TestFactory_NSN:false , TestFactory_OM:false , TestFactory_OTH:false , TestFactory_PM:false , TestFactory_PMC:false , TestFactory_R3:false , TestFactory_R5:false , TestFactory_REF:false , TestFactory_RS: , TestFactory_RSPOS: , TestFactory_RV:false , TestFactory_S3D:false , TestFactory_SAO: , TestFactory_SLO:false , TestFactory_SSR: , TestFactory_SYN:false , TestFactory_TOPMED: , TestFactory_TPA:false , TestFactory_U3:false , TestFactory_U5:false , TestFactory_VC: , TestFactory_VLD:false , TestFactory_VP: , TestFactory_WGT: , TestFactory_WTD:false , TestFactory_dbSNPBuildID: , TestFactory_ID: , TestFactory_FILTER:}, altAllele=TCTTTCCAGT}]) |
0.003s |
passed |
| testCreateFuncotationsOnVariant[3](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/dbSNP_hg19_snippet_with_filters.vcf, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:61662 Q. of type=SNP alleles=[T*, C] attr={} GT=[] filters=, org.broadinstitute.hellbender.engine.ReferenceContext@3df99d5e, [TableFuncotation{dataSourceName='TestFactory', fieldMap={TestFactory_ASP:true , TestFactory_ASS:false , TestFactory_CAF:0.9744,0.02556 , TestFactory_CDA:false , TestFactory_CFL:false , TestFactory_COMMON:1 , TestFactory_DSS:false , TestFactory_G5:true , TestFactory_G5A:false , TestFactory_GENEINFO: , TestFactory_GNO:false , TestFactory_HD:true , TestFactory_INT:false , TestFactory_KGPhase1:true , TestFactory_KGPhase3:true , TestFactory_LSD:false , TestFactory_MTP:false , TestFactory_MUT:false , TestFactory_NOC:false , TestFactory_NOV:false , TestFactory_NSF:false , TestFactory_NSM:false , TestFactory_NSN:false , TestFactory_OM:false , TestFactory_OTH:false , TestFactory_PM:false , TestFactory_PMC:false , TestFactory_R3:false , TestFactory_R5:false , TestFactory_REF:false , TestFactory_RS:73009205 , TestFactory_RSPOS:61662 , TestFactory_RV:false , TestFactory_S3D:false , TestFactory_SAO:0 , TestFactory_SLO:true , TestFactory_SSR:0 , TestFactory_SYN:false , TestFactory_TOPMED:0.954392,0.0456075 , TestFactory_TPA:false , TestFactory_U3:false , TestFactory_U5:false , TestFactory_VC:SNV , TestFactory_VLD:true , TestFactory_VP:0x05010000000515043e000100 , TestFactory_WGT:1 , TestFactory_WTD:false , TestFactory_dbSNPBuildID:130 , TestFactory_ID:rs73009205 , TestFactory_FILTER:FILTER_73}, altAllele=C}]) |
0.004s |
passed |
| testGetAnnotationFeatureClass |
0.002s |
passed |
| testGetName[0]() |
0.002s |
passed |
| testGetName[10](XJ2NYHjJ5n) |
0.001s |
passed |
| testGetName[11](VFZiWJ0ucm3) |
0.001s |
passed |
| testGetName[12](GtWXHA8Frh04) |
0.002s |
passed |
| testGetName[13](IKhzLkBegHu7t) |
0.001s |
passed |
| testGetName[14](2FELUa9xmwxoNe) |
0.001s |
passed |
| testGetName[15](ZMresjHQuFrhCdu) |
0.001s |
passed |
| testGetName[16](AKGfRM985oBnqmrZ) |
0.002s |
passed |
| testGetName[17](6SOctvIEupx1m5TCB) |
0.001s |
passed |
| testGetName[18](QcW3rrckKL5wietLlu) |
0.002s |
passed |
| testGetName[19](yeupyHsy3FoCq62peEM) |
0.001s |
passed |
| testGetName[1](M) |
0.001s |
passed |
| testGetName[2](La) |
0.001s |
passed |
| testGetName[3](EoD) |
0.001s |
passed |
| testGetName[4](5cCe) |
0.002s |
passed |
| testGetName[5](4DmmZ) |
0.001s |
passed |
| testGetName[6](fNCrF2) |
0.001s |
passed |
| testGetName[7](v9WXCWP) |
0.001s |
passed |
| testGetName[8](USQnTmyr) |
0.001s |
passed |
| testGetName[9](4SidtrUVa) |
0.002s |
passed |
| testGetSupportedFuncotationFields |
0.002s |
passed |
| testGetType |
0.001s |
passed |
| testNoSupportOfSegments |
0.003s |
passed |
| testQueryIntoMultiallelic[0](3:69521-69521, [T, C], [{_AC_AMR=0, _AC_Het=0,3,0, _AC=3, _DP_HIST=4891|699|176|41|7229|10522|4675|4512|4936|3378|1833|885|500|250|131|64|34|24|15|139,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|3}]) |
0.006s |
passed |
| testQueryIntoMultiallelic[10](3:13372-13372, [G, T, C], [{_AC_AMR=, _AC_Het=, _AC=, _DP_HIST=}, {_AC_AMR=0, _AC_Het=0, _AC=3, _DP_HIST=14728|2455|2120|518|121|499|534|314|111|21|10|2|2|0|0|0|0|0|0|0,1|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0}]) |
0.004s |
passed |
| testQueryIntoMultiallelic[1](3:69521-69521, [T, A], [{_AC_AMR=2, _AC_Het=0,3,0, _AC=2, _DP_HIST=4891|699|176|41|7229|10522|4675|4512|4936|3378|1833|885|500|250|131|64|34|24|15|139,0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0}]) |
0.004s |
passed |
| testQueryIntoMultiallelic[2](3:69552-69552, [G, A], [{_AC_AMR=0, _AC_Het=1,1,0,0,0,0, _AC=3, _DP_HIST=4764|1048|70|7|7472|10605|4702|4511|4937|3377|1835|886|500|250|128|63|35|22|13|117,0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|1}]) |
0.005s |
passed |
| testQueryIntoMultiallelic[3](3:69552-69552, [G, T], [{_AC_AMR=3, _AC_Het=1,1,0,0,0,0, _AC=3, _DP_HIST=4764|1048|70|7|7472|10605|4702|4511|4937|3377|1835|886|500|250|128|63|35|22|13|117,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|1}]) |
0.004s |
passed |
| testQueryIntoMultiallelic[4](3:69552-69552, [G, C], [{_AC_AMR=0, _AC_Het=1,1,0,0,0,0, _AC=5, _DP_HIST=4764|1048|70|7|7472|10605|4702|4511|4937|3377|1835|886|500|250|128|63|35|22|13|117,3|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0}]) |
0.004s |
passed |
| testQueryIntoMultiallelic[5](3:324682-324714, [ACCAGGCCCAGCTCATGCTTCTTTGCAGCCTCT, A], [{_AC_AMR=0, _AC_Het=1,0,0, _AC=2, _DP_HIST=428|427|186|183|1953|705|127|19|1|2|1|0|0|0|0|0|0|0|0|0,0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0}]) |
0.006s |
passed |
| testQueryIntoMultiallelic[6](3:324682-324714, [ACCAGGCCCAGCTCATGCTTCTTTGCAGCCTCT, TCCAGGCCCAGCTCATGCTTCTTTGCAGCCTCT, A], [{_AC_AMR=0, _AC_Het=1,0,0, _AC=7, _DP_HIST=428|427|186|183|1953|705|127|19|1|2|1|0|0|0|0|0|0|0|0|0,0|0|1|0|1|1|0|1|0|0|0|0|0|0|0|0|0|0|0|0}, {_AC_AMR=0, _AC_Het=1,0,0, _AC=2, _DP_HIST=428|427|186|183|1953|705|127|19|1|2|1|0|0|0|0|0|0|0|0|0,0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0}]) |
0.005s |
passed |
| testQueryIntoMultiallelic[7](3:324682-324682, [A, T], [{_AC_AMR=0, _AC_Het=1,0,0, _AC=7, _DP_HIST=428|427|186|183|1953|705|127|19|1|2|1|0|0|0|0|0|0|0|0|0,0|0|1|0|1|1|0|1|0|0|0|0|0|0|0|0|0|0|0|0}]) |
0.005s |
passed |
| testQueryIntoMultiallelic[8](3:13372-13372, [G, C], [{_AC_AMR=0, _AC_Het=0, _AC=3, _DP_HIST=14728|2455|2120|518|121|499|534|314|111|21|10|2|2|0|0|0|0|0|0|0,1|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0}]) |
0.003s |
passed |
| testQueryIntoMultiallelic[9](3:13372-13372, [G, C, T], [{_AC_AMR=0, _AC_Het=0, _AC=3, _DP_HIST=14728|2455|2120|518|121|499|534|314|111|21|10|2|2|0|0|0|0|0|0|0,1|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0}, {_AC_AMR=, _AC_Het=, _AC=, _DP_HIST=}]) |
0.003s |
passed |
| testRequiresFeatures |
0.001s |
passed |