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VS-1007 - Use default names for VQSR-Lite generated code. #8412
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31aaf3d
Remove some unused VCF header fields from ExtractFeatures
gbggrant 950da0b
Renaming VQS_SENS and related constants back to 'CALIBRATION_SENSITIV…
gbggrant 457aeae
Update dockers and override jar
gbggrant 5b13901
Updated truth path for integration tests
gbggrant d47c639
Update .dockstore.yml with branch names for integration tests.
gbggrant 5dc3dd3
Merge remote-tracking branch 'origin/ah_var_store' into gg_VS-1007_Up…
gbggrant f5c8c3c
Removed entries in .dockstore.yml
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Original file line number | Diff line number | Diff line change |
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@@ -1,18 +1,13 @@ | ||
package org.broadinstitute.hellbender.tools.gvs.common; | ||
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import htsjdk.samtools.SAMSequenceDictionary; | ||
import htsjdk.variant.variantcontext.Allele; | ||
import htsjdk.variant.variantcontext.VariantContext; | ||
import htsjdk.variant.vcf.*; | ||
import htsjdk.variant.vcf.VCFConstants; | ||
import org.apache.commons.lang.StringUtils; | ||
import org.broadinstitute.hellbender.utils.genotyper.IndexedAlleleList; | ||
import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; | ||
import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines; | ||
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import java.util.ArrayList; | ||
import java.util.HashSet; | ||
import java.util.List; | ||
import java.util.Set; | ||
import java.util.stream.Collectors; | ||
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//TODO rename this or get rid of it. a place holder for now | ||
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@@ -53,92 +48,6 @@ public static String getGTString(final VariantContext variant) { | |
return StringUtils.join(gsStrings, separator); | ||
} | ||
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public static VCFHeader generateVcfHeader(Set<String> sampleNames, | ||
final SAMSequenceDictionary sequenceDictionary, | ||
final Set<VCFHeaderLine> extraHeaders) { | ||
final Set<VCFHeaderLine> headerLines = new HashSet<>(); | ||
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headerLines.addAll( getEvoquerVcfHeaderLines() ); | ||
headerLines.addAll( extraHeaders ); | ||
// headerLines.addAll( defaultHeaderLines ); | ||
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final VCFHeader header = new VCFHeader(headerLines, sampleNames); | ||
header.setSequenceDictionary(sequenceDictionary); | ||
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return header; | ||
} | ||
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// TODO is this specific for cohort extract? if so name it such | ||
public static Set<VCFHeaderLine> getEvoquerVcfHeaderLines() { | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Migrated to ExtractFeaturesEngine |
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final Set<VCFHeaderLine> headerLines = new HashSet<>(); | ||
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// TODO: Get a list of all possible values here so that we can make sure they're in the VCF Header! | ||
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// Add standard VCF fields first: | ||
VCFStandardHeaderLines.addStandardInfoLines( headerLines, true, | ||
VCFConstants.STRAND_BIAS_KEY, | ||
VCFConstants.DEPTH_KEY, | ||
VCFConstants.RMS_MAPPING_QUALITY_KEY, | ||
VCFConstants.ALLELE_COUNT_KEY, | ||
VCFConstants.ALLELE_FREQUENCY_KEY, | ||
VCFConstants.ALLELE_NUMBER_KEY, | ||
VCFConstants.END_KEY | ||
); | ||
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VCFStandardHeaderLines.addStandardFormatLines(headerLines, true, | ||
VCFConstants.GENOTYPE_KEY, | ||
VCFConstants.GENOTYPE_QUALITY_KEY, | ||
VCFConstants.DEPTH_KEY, | ||
VCFConstants.GENOTYPE_PL_KEY, | ||
VCFConstants.GENOTYPE_ALLELE_DEPTHS | ||
); | ||
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headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.REFERENCE_GENOTYPE_QUALITY)); | ||
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headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.HAPLOTYPE_CALLER_PHASING_GT_KEY)); | ||
headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.HAPLOTYPE_CALLER_PHASING_ID_KEY)); | ||
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headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_RAW_RMS_MAPPING_QUALITY_KEY)); | ||
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_RMS_MAPPING_QUALITY_KEY)); | ||
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headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_RAW_MAP_QUAL_RANK_SUM_KEY)); | ||
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_MAP_QUAL_RANK_SUM_KEY)); | ||
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headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_RAW_QUAL_APPROX_KEY)); | ||
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.RAW_QUAL_APPROX_KEY)); | ||
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headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_RAW_READ_POS_RANK_SUM_KEY)); | ||
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_READ_POS_RANK_SUM_KEY)); | ||
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headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_SB_TABLE_KEY)); | ||
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.SB_TABLE_KEY)); | ||
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headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_VQS_LOD_KEY)); | ||
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_YNG_STATUS_KEY)); | ||
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headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_VARIANT_DEPTH_KEY)); | ||
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.VARIANT_DEPTH_KEY)); | ||
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headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_STRAND_ODDS_RATIO_KEY)); | ||
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headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_FISHER_STRAND_KEY)); | ||
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headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_QUAL_BY_DEPTH_KEY)); | ||
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.QUAL_BY_DEPTH_KEY)); | ||
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headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.EXCESS_HET_KEY)); | ||
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headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.SB_TABLE_KEY)); | ||
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headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.NAY_FROM_YNG)); | ||
headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.EXCESS_HET_KEY)); | ||
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headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.EXCESS_ALLELES)); | ||
headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.NO_HQ_GENOTYPES)); | ||
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return headerLines; | ||
} | ||
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public enum OutputType { | ||
TSV, | ||
ORC, | ||
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Original file line number | Diff line number | Diff line change |
---|---|---|
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@@ -123,12 +123,6 @@ public static VCFHeaderLine getVqsLodHeader(Double vqsLodThreshold, String model | |
"Site failed " + model + " model VQSLOD cutoff of " + vqsLodThreshold.toString()); | ||
} | ||
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public static VCFHeaderLine getExcessAllelesHeader(int excessAllelesThreshold, String model) { | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Unreferenced header field |
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// should there be a gate for max or min excessAllelesThreshold value? | ||
return new VCFFilterHeaderLine(GATKVCFConstants.VQSR_FAILURE_PREFIX + model, | ||
"Site failed " + model + " model excess allele cutoff (" + excessAllelesThreshold + ")"); | ||
} | ||
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public static VCFHeaderLine getTruthSensitivityHeader(Double truthSensitivityThreshold, Double vqsLodThreshold, String model) { | ||
if (truthSensitivityThreshold == null) { // at this point, we know that all vqsr threshold inputs are null, so use defaults | ||
truthSensitivityThreshold = GATKVCFConstants.SNP.contains(model) ? DEFAULT_TRUTH_SENSITIVITY_THRESHOLD_SNPS : DEFAULT_TRUTH_SENSITIVITY_THRESHOLD_INDELS; | ||
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Migrated to ExtractFeaturesEngine