Class org.broadinstitute.hellbender.tools.funcotator.FuncotationMapUnitTest

all > org.broadinstitute.hellbender.tools.funcotator > FuncotationMapUnitTest
46

tests
0

failures
0

ignored
1.112s

duration
100%

successful

Tests

Test Duration Result
testAddAndGet[0](chr3, 178916538, 178916538, G, C, /tmp/funcotatorTmpFolder8495968578938350762/GRCh37.p13.chr3.fasta, org.broadinstitute.hellbender.engine.ReferenceFileSource@75ac326f, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf, ALL, [ENST00000263967.3], [TableFuncotation{dataSourceName='TestDataSource5', fieldMap={TESTFIELD1:ETESTFIELD1value , TESTADD:ETESTADDvalue}, altAllele=A}, TableFuncotation{dataSourceName='TestDataSource5', fieldMap={TESTFIELD1:FTESTFIELD1value , TESTADD:FTESTADDvalue}, altAllele=AG}, TableFuncotation{dataSourceName='TestDataSource5', fieldMap={TESTFIELD1:GTESTFIELD1value , TESTADD:GTESTADDvalue}, altAllele=AT}]) 0.220s passed
testAddAndGet[1](chr19, 8994200, 8994200, G, C, /tmp/funcotatorTmpFolder10615787711409872845/GRCh37.p13.chr19.fasta, org.broadinstitute.hellbender.engine.ReferenceFileSource@58e7f930, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf, BEST_EFFECT, [ENST00000397910.4], [TableFuncotation{dataSourceName='TestDataSource5', fieldMap={TESTFIELD1:ETESTFIELD1value , TESTADD:ETESTADDvalue}, altAllele=A}, TableFuncotation{dataSourceName='TestDataSource5', fieldMap={TESTFIELD1:FTESTFIELD1value , TESTADD:FTESTADDvalue}, altAllele=AG}, TableFuncotation{dataSourceName='TestDataSource5', fieldMap={TESTFIELD1:GTESTFIELD1value , TESTADD:GTESTADDvalue}, altAllele=AT}]) 0.116s passed
testAddAndGet[2](chr19, 8994200, 8994200, G, C, /tmp/funcotatorTmpFolder10615787711409872845/GRCh37.p13.chr19.fasta, org.broadinstitute.hellbender.engine.ReferenceFileSource@7c460, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf, ALL, [ENST00000397910.4, ENST00000380951.5], [TableFuncotation{dataSourceName='TestDataSource5', fieldMap={TESTFIELD1:ETESTFIELD1value , TESTADD:ETESTADDvalue}, altAllele=A}, TableFuncotation{dataSourceName='TestDataSource5', fieldMap={TESTFIELD1:FTESTFIELD1value , TESTADD:FTESTADDvalue}, altAllele=AG}, TableFuncotation{dataSourceName='TestDataSource5', fieldMap={TESTFIELD1:GTESTFIELD1value , TESTADD:GTESTADDvalue}, altAllele=AT}]) 0.101s passed
testAddingGencodeFuncotationToFuncotationMap 0.094s passed
testCopy 0.012s passed
testCopyWithGencode 0.002s passed
testCreateNoTranscriptInfo[0]([TableFuncotation{dataSourceName='Gencode', fieldMap={FOO:AFOOvalue , BAR:ABARvalue}, altAllele=T}]) 0.001s passed
testCreateNoTranscriptInfo[1]([TableFuncotation{dataSourceName='Gencode', fieldMap={FOO:BFOOvalue , BAR:BBARvalue}, altAllele=C}]) 0s passed
testCreateNoTranscriptInfo[2]([TableFuncotation{dataSourceName='Gencode', fieldMap={FOO:CFOOvalue , BAR:CBARvalue}, altAllele=GG}]) 0s passed
testCreateNoTranscriptInfo[3]([TableFuncotation{dataSourceName='TestDataSource4', fieldMap={FOO:DFOOvalue , BAR:DBARvalue}, altAllele=T}]) 0.001s passed
testCreateNoTranscriptInfo[4]([TableFuncotation{dataSourceName='TestDataSource5', fieldMap={FOO:EFOOvalue , BAR:EBARvalue}, altAllele=A}, TableFuncotation{dataSourceName='TestDataSource5', fieldMap={FOO:FFOOvalue , BAR:FBARvalue}, altAllele=AG}, TableFuncotation{dataSourceName='TestDataSource5', fieldMap={FOO:GFOOvalue , BAR:GBARvalue}, altAllele=AT}]) 0s passed
testCreationFromFuncotationVcfHeaderString[0](C, FOO, Functional annotation from the Funcotator tool. Funcotation fields are: Gencode_19_hugoSymbol|Gencode_19_ncbiBuild|Gencode_19_chromosome, [FOO|hg19|4], [no_transcript], [{Gencode_19_chromosome=4, Gencode_19_hugoSymbol=FOO, Gencode_19_ncbiBuild=hg19}]) 0.001s passed
testCreationFromFuncotationVcfHeaderString[10](AT, TEST, Functional annotation from the Funcotator tool. Funcotation fields are: Gencode_19_hugoSymbol|Gencode_19_ncbiBuild|Gencode_19_chromosome, [FOO|hg19|4], [no_transcript], [{Gencode_19_chromosome=4, Gencode_19_hugoSymbol=FOO, Gencode_19_ncbiBuild=hg19}]) 0s passed
testCreationFromFuncotationVcfHeaderString[11](AT, BAZ, Functional annotation from the Funcotator tool. Funcotation fields are: Gencode_19_hugoSymbol|Gencode_19_ncbiBuild|Gencode_19_chromosome, [FOO|hg19|], [no_transcript], [{Gencode_19_chromosome=, Gencode_19_hugoSymbol=FOO, Gencode_19_ncbiBuild=hg19}]) 0s passed
testCreationFromFuncotationVcfHeaderString[12](AT, BAZ, Functional annotation from the Funcotator tool. Funcotation fields are: Gencode_19_hugoSymbol|Gencode_19_ncbiBuild|Gencode_19_chromosome, [|hg19|4], [no_transcript], [{Gencode_19_chromosome=4, Gencode_19_hugoSymbol=, Gencode_19_ncbiBuild=hg19}]) 0s passed
testCreationFromFuncotationVcfHeaderString[13](AT, BAZ, Functional annotation from the Funcotator tool. Funcotation fields are: Gencode_19_hugoSymbol|Gencode_19_ncbiBuild|Gencode_19_annotationTranscript, [FOO|hg19|txID1]#[BAR|hg38|txID2], [txID1, txID2], [{Gencode_19_annotationTranscript=txID1, Gencode_19_hugoSymbol=FOO, Gencode_19_ncbiBuild=hg19}, {Gencode_19_annotationTranscript=txID2, Gencode_19_hugoSymbol=BAR, Gencode_19_ncbiBuild=hg38}]) 0.001s passed
testCreationFromFuncotationVcfHeaderString[14](AT, BAZ, Functional annotation from the Funcotator tool. Funcotation fields are: Gencode_19_hugoSymbol|Gencode_19_ncbiBuild|Gencode_19_annotationTranscript, [FOO|hg19|txID1]#[BAR|hg38|txID2]#[BAZ|hg38|txID3], [txID1, txID2, txID3], [{Gencode_19_annotationTranscript=txID1, Gencode_19_hugoSymbol=FOO, Gencode_19_ncbiBuild=hg19}, {Gencode_19_annotationTranscript=txID2, Gencode_19_hugoSymbol=BAR, Gencode_19_ncbiBuild=hg38}, {Gencode_19_annotationTranscript=txID3, Gencode_19_hugoSymbol=BAZ, Gencode_19_ncbiBuild=hg38}]) 0s passed
testCreationFromFuncotationVcfHeaderString[15](CATATAT, TEST, Functional annotation from the Funcotator tool. Funcotation fields are: Gencode_28_hugoSymbol|Gencode_28_ncbiBuild|Gencode_28_chromosome|Gencode_28_start|Gencode_28_end|Gencode_28_variantClassification|Gencode_28_secondaryVariantClassification|Gencode_28_variantType|Gencode_28_refAllele|Gencode_28_tumorSeqAllele1|Gencode_28_tumorSeqAllele2|Gencode_28_genomeChange|Gencode_28_annotationTranscript|Gencode_28_transcriptStrand|Gencode_28_transcriptExon|Gencode_28_transcriptPos|Gencode_28_cDnaChange|Gencode_28_codonChange|Gencode_28_proteinChange|Gencode_28_gcContent|Gencode_28_referenceContext|Gencode_28_otherTranscripts|dummy_ClinVar_VCF_AC|dummy_ClinVar_VCF_AF|dummy_ClinVar_VCF_AF_ESP|dummy_ClinVar_VCF_AF_EXAC|dummy_ClinVar_VCF_AF_TGP|dummy_ClinVar_VCF_ALLELEID|dummy_ClinVar_VCF_AN|dummy_ClinVar_VCF_CLNDISDB|dummy_ClinVar_VCF_CLNDISDBINCL|dummy_ClinVar_VCF_CLNDN|dummy_ClinVar_VCF_CLNDNINCL|dummy_ClinVar_VCF_CLNHGVS|dummy_ClinVar_VCF_CLNREVSTAT|dummy_ClinVar_VCF_CLNSIG|dummy_ClinVar_VCF_CLNSIGCONF|dummy_ClinVar_VCF_CLNSIGINCL|dummy_ClinVar_VCF_CLNVC|dummy_ClinVar_VCF_CLNVCSO|dummy_ClinVar_VCF_CLNVI|dummy_ClinVar_VCF_DBVARID|dummy_ClinVar_VCF_DP|dummy_ClinVar_VCF_GENEINFO|dummy_ClinVar_VCF_MC|dummy_ClinVar_VCF_ORIGIN|dummy_ClinVar_VCF_RS|dummy_ClinVar_VCF_SSR, [||chr3|179135392|179135393|IGR||INS|-|-|AT||no_transcript|+||||||0.3292079207920792|AAAATGTGATCATATATATATATATATATAT|||||||||||||||||||||||||||], [no_transcript], [{Gencode_28_annotationTranscript=no_transcript, Gencode_28_cDnaChange=, Gencode_28_chromosome=chr3, Gencode_28_codonChange=, Gencode_28_end=179135393, Gencode_28_gcContent=0.329207921, Gencode_28_genomeChange=, Gencode_28_hugoSymbol=, Gencode_28_ncbiBuild=, Gencode_28_otherTranscripts=, Gencode_28_proteinChange=, Gencode_28_refAllele=-, Gencode_28_referenceContext=AAAATGTGATCATATATATATATATATATAT, Gencode_28_secondaryVariantClassification=, Gencode_28_start=179135392, Gencode_28_transcriptExon=, Gencode_28_transcriptPos=, Gencode_28_transcriptStrand=+, Gencode_28_tumorSeqAllele1=-, Gencode_28_tumorSeqAllele2=AT, Gencode_28_variantClassification=IGR, Gencode_28_variantType=INS, dummy_ClinVar_VCF_AC=, dummy_ClinVar_VCF_AF=, dummy_ClinVar_VCF_AF_ESP=, dummy_ClinVar_VCF_AF_EXAC=, dummy_ClinVar_VCF_AF_TGP=, dummy_ClinVar_VCF_ALLELEID=, dummy_ClinVar_VCF_AN=, dummy_ClinVar_VCF_CLNDISDB=, dummy_ClinVar_VCF_CLNDISDBINCL=, dummy_ClinVar_VCF_CLNDN=, dummy_ClinVar_VCF_CLNDNINCL=, dummy_ClinVar_VCF_CLNHGVS=, dummy_ClinVar_VCF_CLNREVSTAT=, dummy_ClinVar_VCF_CLNSIG=, dummy_ClinVar_VCF_CLNSIGCONF=, dummy_ClinVar_VCF_CLNSIGINCL=, dummy_ClinVar_VCF_CLNVC=, dummy_ClinVar_VCF_CLNVCSO=, dummy_ClinVar_VCF_CLNVI=, dummy_ClinVar_VCF_DBVARID=, dummy_ClinVar_VCF_DP=, dummy_ClinVar_VCF_GENEINFO=, dummy_ClinVar_VCF_MC=, dummy_ClinVar_VCF_ORIGIN=, dummy_ClinVar_VCF_RS=, dummy_ClinVar_VCF_SSR=}]) 0.001s passed
testCreationFromFuncotationVcfHeaderString[1](C, FOO, Functional annotation from the Funcotator tool. Funcotation fields are: Gencode_19_hugoSymbol|Gencode_19_ncbiBuild|Gencode_19_chromosome, [FOO|hg19|], [no_transcript], [{Gencode_19_chromosome=, Gencode_19_hugoSymbol=FOO, Gencode_19_ncbiBuild=hg19}]) 0.001s passed
testCreationFromFuncotationVcfHeaderString[2](C, FOO, Functional annotation from the Funcotator tool. Funcotation fields are: Gencode_19_hugoSymbol|Gencode_19_ncbiBuild|Gencode_19_chromosome, [|hg19|4], [no_transcript], [{Gencode_19_chromosome=4, Gencode_19_hugoSymbol=, Gencode_19_ncbiBuild=hg19}]) 0s passed
testCreationFromFuncotationVcfHeaderString[3](C, TEST, Functional annotation from the Funcotator tool. Funcotation fields are: Gencode_19_hugoSymbol|Gencode_19_ncbiBuild|Gencode_19_annotationTranscript, [FOO|hg19|txID1]#[BAR|hg38|txID2], [txID1, txID2], [{Gencode_19_annotationTranscript=txID1, Gencode_19_hugoSymbol=FOO, Gencode_19_ncbiBuild=hg19}, {Gencode_19_annotationTranscript=txID2, Gencode_19_hugoSymbol=BAR, Gencode_19_ncbiBuild=hg38}]) 0s passed
testCreationFromFuncotationVcfHeaderString[4](C, TEST, Functional annotation from the Funcotator tool. Funcotation fields are: Gencode_19_hugoSymbol|Gencode_19_ncbiBuild|Gencode_19_annotationTranscript, [FOO|hg19|txID1]#[BAR|hg38|txID2]#[BAZ|hg38|txID3], [txID1, txID2, txID3], [{Gencode_19_annotationTranscript=txID1, Gencode_19_hugoSymbol=FOO, Gencode_19_ncbiBuild=hg19}, {Gencode_19_annotationTranscript=txID2, Gencode_19_hugoSymbol=BAR, Gencode_19_ncbiBuild=hg38}, {Gencode_19_annotationTranscript=txID3, Gencode_19_hugoSymbol=BAZ, Gencode_19_ncbiBuild=hg38}]) 0s passed
testCreationFromFuncotationVcfHeaderString[5](A, TEST, Functional annotation from the Funcotator tool. Funcotation fields are: Gencode_19_hugoSymbol|Gencode_19_ncbiBuild|Gencode_19_chromosome, [FOO|hg19|4], [no_transcript], [{Gencode_19_chromosome=4, Gencode_19_hugoSymbol=FOO, Gencode_19_ncbiBuild=hg19}]) 0s passed
testCreationFromFuncotationVcfHeaderString[6](A, TEST, Functional annotation from the Funcotator tool. Funcotation fields are: Gencode_19_hugoSymbol|Gencode_19_ncbiBuild|Gencode_19_chromosome, [FOO|hg19|], [no_transcript], [{Gencode_19_chromosome=, Gencode_19_hugoSymbol=FOO, Gencode_19_ncbiBuild=hg19}]) 0s passed
testCreationFromFuncotationVcfHeaderString[7](A, TEST, Functional annotation from the Funcotator tool. Funcotation fields are: Gencode_19_hugoSymbol|Gencode_19_ncbiBuild|Gencode_19_chromosome, [|hg19|4], [no_transcript], [{Gencode_19_chromosome=4, Gencode_19_hugoSymbol=, Gencode_19_ncbiBuild=hg19}]) 0.001s passed
testCreationFromFuncotationVcfHeaderString[8](A, TEST, Functional annotation from the Funcotator tool. Funcotation fields are: Gencode_19_hugoSymbol|Gencode_19_ncbiBuild|Gencode_19_annotationTranscript, [FOO|hg19|txID1]#[BAR|hg38|txID2], [txID1, txID2], [{Gencode_19_annotationTranscript=txID1, Gencode_19_hugoSymbol=FOO, Gencode_19_ncbiBuild=hg19}, {Gencode_19_annotationTranscript=txID2, Gencode_19_hugoSymbol=BAR, Gencode_19_ncbiBuild=hg38}]) 0s passed
testCreationFromFuncotationVcfHeaderString[9](A, TEST, Functional annotation from the Funcotator tool. Funcotation fields are: Gencode_19_hugoSymbol|Gencode_19_ncbiBuild|Gencode_19_annotationTranscript, [FOO|hg19|txID1]#[BAR|hg38|txID2]#[BAZ|hg38|txID3], [txID1, txID2, txID3], [{Gencode_19_annotationTranscript=txID1, Gencode_19_hugoSymbol=FOO, Gencode_19_ncbiBuild=hg19}, {Gencode_19_annotationTranscript=txID2, Gencode_19_hugoSymbol=BAR, Gencode_19_ncbiBuild=hg38}, {Gencode_19_annotationTranscript=txID3, Gencode_19_hugoSymbol=BAZ, Gencode_19_ncbiBuild=hg38}]) 0s passed
testDoAllTxAlleleCombinationsHaveTheSameFields[0](org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@66698de2, {no_transcript=[FIELD7, FIELD8]}, true, {no_transcript=[C]}) 0.001s passed
testDoAllTxAlleleCombinationsHaveTheSameFields[1](org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@308dd573, {TX1=[FIELD2, FIELD1], TX2=[FIELD2, FIELD1]}, true, {TX1=[A, AG, AT], TX2=[A, AG, AT]}) 0.001s passed
testDoAllTxAlleleCombinationsHaveTheSameFields[2](org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@4b64cd71, {TX1=[FIELD2, FIELD3, FIELD4, FIELD5, FIELD6, FIELD1], TX2=[FIELD7, FIELD8]}, false, {TX1=[A, AG, AT], TX2=[C]}) 0s passed
testGencodeFuncotationCreation[0](chr3, 178916538, 178916538, G, C, /tmp/funcotatorTmpFolder8495968578938350762/GRCh37.p13.chr3.fasta, org.broadinstitute.hellbender.engine.ReferenceFileSource@16cbba0f, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf, ALL, [ENST00000263967.3]) 0.088s passed
testGencodeFuncotationCreation[1](chr3, 178916538, 178916538, G, C, /tmp/funcotatorTmpFolder8495968578938350762/GRCh37.p13.chr3.fasta, org.broadinstitute.hellbender.engine.ReferenceFileSource@dddcd91, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf, CANONICAL, [ENST00000263967.3]) 0.089s passed
testGencodeFuncotationCreation[2](chr19, 8994200, 8994200, G, C, /tmp/funcotatorTmpFolder10615787711409872845/GRCh37.p13.chr19.fasta, org.broadinstitute.hellbender.engine.ReferenceFileSource@575e862c, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf, ALL, [ENST00000397910.4, ENST00000380951.5]) 0.089s passed
testGencodeFuncotationCreation[3](chr19, 9014550, 9014550, T, A, /tmp/funcotatorTmpFolder10615787711409872845/GRCh37.p13.chr19.fasta, org.broadinstitute.hellbender.engine.ReferenceFileSource@1aee6983, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf, ALL, [ENST00000397910.4]) 0.087s passed
testGencodeFuncotationCreation[4](chr19, 8994200, 8994200, G, C, /tmp/funcotatorTmpFolder10615787711409872845/GRCh37.p13.chr19.fasta, org.broadinstitute.hellbender.engine.ReferenceFileSource@448a6d00, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf, CANONICAL, [ENST00000397910.4]) 0.087s passed
testGencodeFuncotationCreation[5](chr19, 8994200, 8994200, G, C, /tmp/funcotatorTmpFolder10615787711409872845/GRCh37.p13.chr19.fasta, org.broadinstitute.hellbender.engine.ReferenceFileSource@d28a235, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa, /home/runner/work/gatk/gatk/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf, BEST_EFFECT, [ENST00000397910.4]) 0.087s passed
testGetAlleles[0](org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@66698de2, {no_transcript=[FIELD7, FIELD8]}, true, {no_transcript=[C]}) 0s passed
testGetAlleles[1](org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@308dd573, {TX1=[FIELD2, FIELD1], TX2=[FIELD2, FIELD1]}, true, {TX1=[A, AG, AT], TX2=[A, AG, AT]}) 0s passed
testGetAlleles[2](org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@4b64cd71, {TX1=[FIELD2, FIELD3, FIELD4, FIELD5, FIELD6, FIELD1], TX2=[FIELD7, FIELD8]}, false, {TX1=[A, AG, AT], TX2=[C]}) 0s passed
testGetFieldNames[0](org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@66698de2, {no_transcript=[FIELD7, FIELD8]}, true, {no_transcript=[C]}) 0.001s passed
testGetFieldNames[1](org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@308dd573, {TX1=[FIELD2, FIELD1], TX2=[FIELD2, FIELD1]}, true, {TX1=[A, AG, AT], TX2=[A, AG, AT]}) 0s passed
testGetFieldNames[2](org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@4b64cd71, {TX1=[FIELD2, FIELD3, FIELD4, FIELD5, FIELD6, FIELD1], TX2=[FIELD7, FIELD8]}, false, {TX1=[A, AG, AT], TX2=[C]}) 0s passed
testMultiAlleleicFuncotationMapCreation 0.026s passed
testSerializationRoundTrip 0.003s passed
testTranscriptListAndSetAreOrdered[0]([org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@53816ff7]) 0s passed
testTranscriptListAndSetAreOrdered[1]([org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@38d1e9c4, org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@8fefdaa3, org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@e70dcb82, org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@3e2bbc61, org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@9549ad40, org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@ec679e1f, org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@43858efe, org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@9aa37fdd, org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@f1c170bc, org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@a672b8b8, org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@fd90a997, org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@54ae9a76, org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@abcc8b55, org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@2ea7c34, org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@5a086d13, org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@b1265df2, org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation@8444ed1]) 0.001s passed

Standard error

17:39:22.324 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: -, alt = G, ref C != T reference coding seq) @[chr19:8994200]!  Substituting given allele for sequence code (TTG->CTG)
17:39:22.333 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: -, alt = G, ref C != T reference coding seq) @[chr19:8994200]!  Substituting given allele for sequence code (TTG->CTG)
17:39:22.430 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: -, alt = G, ref C != T reference coding seq) @[chr19:8994200]!  Substituting given allele for sequence code (TTG->CTG)
17:39:22.434 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: -, alt = G, ref C != T reference coding seq) @[chr19:8994200]!  Substituting given allele for sequence code (TTG->CTG)
17:39:22.525 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: -, alt = G, ref C != T reference coding seq) @[chr19:8994200]!  Substituting given allele for sequence code (TTG->CTG)
17:39:22.528 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: -, alt = G, ref C != T reference coding seq) @[chr19:8994200]!  Substituting given allele for sequence code (TTG->CTG)
17:39:22.823 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: -, alt = G, ref C != T reference coding seq) @[chr19:8994200]!  Substituting given allele for sequence code (TTG->CTG)
17:39:22.825 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: -, alt = G, ref C != T reference coding seq) @[chr19:8994200]!  Substituting given allele for sequence code (TTG->CTG)
17:39:22.997 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: -, alt = G, ref C != T reference coding seq) @[chr19:8994200]!  Substituting given allele for sequence code (TTG->CTG)
17:39:22.999 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: -, alt = G, ref C != T reference coding seq) @[chr19:8994200]!  Substituting given allele for sequence code (TTG->CTG)
17:39:23.084 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: -, alt = G, ref C != T reference coding seq) @[chr19:8994200]!  Substituting given allele for sequence code (TTG->CTG)
17:39:23.086 WARN  FuncotatorUtils - Reference allele is different than the reference coding sequence (strand: -, alt = G, ref C != T reference coding seq) @[chr19:8994200]!  Substituting given allele for sequence code (TTG->CTG)