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DRAFT: VCFHeader refactoring #1880

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DRAFT: VCFHeader refactoring #1880

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fc85c75
Changes for the htsjdk VCFHeader and VCFHeaderLine refactoring.
cmnbroad Oct 17, 2021
b38406a
Update header merging.
cmnbroad May 17, 2023
2c4f232
Temporarily use htsjdk snapshot.
cmnbroad May 17, 2023
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2 changes: 1 addition & 1 deletion build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ def ensureBuildPrerequisites(buildPrerequisitesMessage) {

ensureBuildPrerequisites(buildPrerequisitesMessage)

final htsjdkVersion = System.getProperty('htsjdk.version', '3.0.1')
final htsjdkVersion = System.getProperty('htsjdk.version', '3.0.5-12-g5700958-SNAPSHOT')
final googleNio = 'com.google.cloud:google-cloud-nio:0.123.25'

configurations {
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2 changes: 1 addition & 1 deletion src/main/java/picard/fingerprint/FingerprintUtils.java
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Expand Up @@ -95,7 +95,7 @@ private static VariantContextWriter getVariantContextWriter(final File outputFil
.setReferenceDictionary(ref.getSequenceDictionary())
.setOutputFile(outputFile).build();

final Set<VCFHeaderLine> lines = new LinkedHashSet<>();
final Set<VCFHeaderLine> lines = VCFHeader.makeHeaderVersionLineSet(VCFHeader.DEFAULT_VCF_VERSION);
lines.add(new VCFHeaderLine("reference", referenceSequenceFileName.getAbsolutePath()));
lines.add(new VCFHeaderLine("source", source));
lines.add(new VCFHeaderLine("fileDate", new Date().toString()));
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7 changes: 3 additions & 4 deletions src/main/java/picard/fingerprint/HaplotypeMap.java
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Expand Up @@ -369,12 +369,11 @@ public void writeAsVcf(final File output, final File refFile) throws FileNotFoun
.build()) {

final VCFHeader vcfHeader = new VCFHeader(
VCFUtils.withUpdatedContigsAsLines(Collections.emptySet(), refFile, header.getSequenceDictionary(), false),
VCFUtils.withUpdatedContigsAsLines(
VCFHeader.makeHeaderVersionLineSet(VCFHeader.DEFAULT_VCF_VERSION),
refFile, header.getSequenceDictionary(), false),
Collections.singleton(HET_GENOTYPE_FOR_PHASING));

VCFUtils.withUpdatedContigsAsLines(Collections.emptySet(), refFile, header.getSequenceDictionary(), false);

vcfHeader.addMetaDataLine(new VCFHeaderLine(VCFHeaderVersion.VCF4_2.getFormatString(), VCFHeaderVersion.VCF4_2.getVersionString()));
vcfHeader.addMetaDataLine(new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"));
vcfHeader.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
vcfHeader.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.PHASE_SET_KEY, 1, VCFHeaderLineType.String, "Phase-set identifier for phased genotypes."));
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12 changes: 2 additions & 10 deletions src/main/java/picard/vcf/GenotypeConcordance.java
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Expand Up @@ -40,13 +40,7 @@
import htsjdk.variant.variantcontext.writer.Options;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder;
import htsjdk.variant.vcf.VCFConstants;
import htsjdk.variant.vcf.VCFFileReader;
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFHeaderLine;
import htsjdk.variant.vcf.VCFHeaderLineCount;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import htsjdk.variant.vcf.*;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
import org.broadinstitute.barclay.help.DocumentedFeature;
Expand Down Expand Up @@ -497,9 +491,7 @@ private Optional<VariantContextWriter> getVariantContextWriter(final VCFFileRead

// create the output header
final List<String> sampleNames = Arrays.asList(OUTPUT_VCF_CALL_SAMPLE_NAME, OUTPUT_VCF_TRUTH_SAMPLE_NAME);
final Set<VCFHeaderLine> headerLines = new HashSet<>();
headerLines.addAll(callReader.getFileHeader().getMetaDataInInputOrder());
headerLines.addAll(truthReader.getFileHeader().getMetaDataInInputOrder());
final Set<VCFHeaderLine> headerLines = VCFHeaderMerger.getMergedHeaderLines(Arrays.asList(callReader.getFileHeader(), truthReader.getFileHeader()), true);
headerLines.add(CONTINGENCY_STATE_HEADER_LINE);
writer.writeHeader(new VCFHeader(headerLines, sampleNames));
return Optional.of(writer);
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