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Fixed a bug with END positions for deletions in MAF output. #5876

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Apr 11, 2019
Merged

Fixed a bug with END positions for deletions in MAF output. #5876

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9 changes: 7 additions & 2 deletions ...main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRenderer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -480,12 +480,17 @@ else if ( refAlleleLength > altAlleleLength ) {
// Remove the first N bases from the Tumor_Seq_Allele1
// Replace the alt_allele with "-"
// Increment the Start_Position by 1 (start position should be inclusive of the first base deleted)
// Increment the End_Position by M-1 where M = length(ref_allele) (end position should be inclusive of the last base deleted)
// Set the End_Position to Start_Position + M - 2, where M = length(ref_allele) (end position should be inclusive of the last base deleted, explanation below)
outputMap.put(MafOutputRendererConstants.FieldName_Reference_Allele, outputMap.get(MafOutputRendererConstants.FieldName_Reference_Allele).substring(altAlleleLength));
outputMap.put(MafOutputRendererConstants.FieldName_Tumor_Seq_Allele1, outputMap.get(MafOutputRendererConstants.FieldName_Tumor_Seq_Allele1).substring(altAlleleLength));
outputMap.put(MafOutputRendererConstants.FieldName_Tumor_Seq_Allele2, MafOutputRendererConstants.EmptyAllele);
outputMap.put(MafOutputRendererConstants.FieldName_Start_Position, String.valueOf(Integer.valueOf(outputMap.get(MafOutputRendererConstants.FieldName_Start_Position)) + 1));
outputMap.put(MafOutputRendererConstants.FieldName_End_Position, String.valueOf(Integer.valueOf(outputMap.get(MafOutputRendererConstants.FieldName_End_Position)) + refAlleleLength - 1));

// Use the new start position we just calculated for this end position.
// Then subtract 2 from ref allele length:
// -1 for the removed first base
// -1 for the inclusive nature of positions
outputMap.put(MafOutputRendererConstants.FieldName_End_Position, String.valueOf(Integer.valueOf(outputMap.get(MafOutputRendererConstants.FieldName_Start_Position)) + refAlleleLength - 2));
}
}
}
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23 changes: 23 additions & 0 deletions ...a/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRendererUnitTest.java
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Expand Up @@ -379,6 +379,29 @@ private Object[][] provideForAdjustIndelAlleleInformationForMafOutput() {
}
)
},
// Map contains a DELETION of size 3 with associated fields:
{
MapUtils.putAll(new LinkedHashMap<String, String>(),
new Object[][] {
{ MafOutputRendererConstants.FieldName_Variant_Type, GencodeFuncotation.VariantType.DEL.toString() },
{ MafOutputRendererConstants.FieldName_Reference_Allele, "CAGG" },
{ MafOutputRendererConstants.FieldName_Tumor_Seq_Allele1, "CAGG" },
{ MafOutputRendererConstants.FieldName_Tumor_Seq_Allele2, "C" },
{ MafOutputRendererConstants.FieldName_Start_Position, "2222103" },
{ MafOutputRendererConstants.FieldName_End_Position, "2222103" },
}
),
MapUtils.putAll(new LinkedHashMap<String, String>(),
new Object[][] {
{ MafOutputRendererConstants.FieldName_Variant_Type, GencodeFuncotation.VariantType.DEL.toString() },
{ MafOutputRendererConstants.FieldName_Reference_Allele, "AGG" },
{ MafOutputRendererConstants.FieldName_Tumor_Seq_Allele1, "AGG" },
{ MafOutputRendererConstants.FieldName_Tumor_Seq_Allele2, "-" },
{ MafOutputRendererConstants.FieldName_Start_Position, "2222104" },
{ MafOutputRendererConstants.FieldName_End_Position, "2222106" },
}
)
},
};
}

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230 changes: 115 additions & 115 deletions ...itute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large_expected.maf
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2 changes: 1 addition & 1 deletion ...itute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large_expected.vcf
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Expand Up @@ -25,7 +25,7 @@
##FORMAT=<ID=Y,Number=1,Type=Integer,Description="Raw Y intensity">
##Funcotator Version=0.0.4 | Gencode 19 CANONICAL | Achilles 110303 | CGC full_2012_03-15 | ClinVar 12.03.20 | Cosmic v84 | CosmicFusion v84 | CosmicTissue v83 | DNARepairGenes 20180524T145835 | Familial_Cancer_Genes 20110905 | Gencode_XHGNC 75_37 | Gencode_XRefSeq 75_37 | HGNC Nov302017 | Oreganno 20160119 | Simple_Uniprot 2014_12 | dbSNP 9606_b150
##Funcotator Version=Unavailable | Gencode 19 CANONICAL | Achilles 110303 | CGC full_2012_03-15 | ClinVar 12.03.20 | Cosmic 83 | CosmicFusion v83 | CosmicTissue v83 | DNARepairGenes 20171217T214737 | Familial_Cancer_Genes 20110905 | Gencode_XHGNC 75_37 | Gencode_XRefSeq 75_37 | HGNC Nov302017 | Simple_Uniprot 2014_12 | dbSNP 9606_b150
##GATKCommandLine=<ID=Funcotator,CommandLine="Funcotator --output /var/folders/4p/2b7bzvcx0x7bxvbztmwk__6rkr9cxg/T/regressionTestHg19Large.vcf.funcotator7518371726207473318.vcf --ref-version hg19 --data-sources-path /Users/jonn/Development/gatk/src/test/resources/large/funcotator/funcotator_dataSources/ --output-file-format VCF --variant /Users/jonn/Development/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large.vcf --reference /Users/jonn/Development/gatk/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz --verbosity INFO --remove-filtered-variants false --transcript-selection-mode CANONICAL --five-prime-flank-size 5000 --three-prime-flank-size 0 --lookahead-cache-bp 100000 --force-b37-to-hg19-reference-contig-conversion false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version=Unavailable,Date="March 25, 2019 12:39:04 PM EDT">
##GATKCommandLine=<ID=Funcotator,CommandLine="Funcotator --output /var/folders/4p/2b7bzvcx0x7bxvbztmwk__6rkr9cxg/T/regressionTestHg19Large.vcf.funcotator5488422217831794739.vcf --ref-version hg19 --data-sources-path /Users/jonn/Development/gatk/src/test/resources/large/funcotator/funcotator_dataSources/ --output-file-format VCF --variant /Users/jonn/Development/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large.vcf --reference /Users/jonn/Development/gatk/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz --verbosity INFO --remove-filtered-variants false --transcript-selection-mode CANONICAL --five-prime-flank-size 5000 --three-prime-flank-size 0 --lookahead-cache-bp 100000 --force-b37-to-hg19-reference-contig-conversion false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="Unavailable",Date="April 11, 2019 10:49:42 AM EDT">
##GATKCommandLine=<ID=Funcotator,CommandLine="Funcotator --output FUNCOTATOR_OUT.vcf --ref-version hg19 --data-sources-path /Users/jonn/Development/funcotator_dataSources_latest --output-file-format VCF --variant /Users/jonn/Development/NON_PUBLIC/0816201804HC0_R01C01.vcf --reference /Users/jonn/Development/references/Homo_sapiens_assembly19.fasta --verbosity DEBUG --remove-filtered-variants false --transcript-selection-mode CANONICAL --lookahead-cache-bp 100000 --force-b37-to-hg19-reference-contig-conversion false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version=4.0.10.1-17-g2de000f-SNAPSHOT-0.0.4,Date="October 19, 2018 2:12:35 PM EDT">
##Hyb(High)=Hyb(High)|Hybridization|3310|11184
##Hyb(Low)=Hyb(Low)|Hybridization|3436|1823
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