Skip to content
Draft
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion build.gradle
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 {
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/picard/fingerprint/FingerprintUtils.java
Original file line number Diff line number Diff line change
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()));
Expand Down
7 changes: 3 additions & 4 deletions src/main/java/picard/fingerprint/HaplotypeMap.java
Original file line number Diff line number Diff line change
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."));
Expand Down
12 changes: 2 additions & 10 deletions src/main/java/picard/vcf/GenotypeConcordance.java
Original file line number Diff line number Diff line change
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);
Expand Down
Loading