Java Code Examples for htsjdk.variant.vcf.VCFHeader#getMetaDataInInputOrder()
The following examples show how to use
htsjdk.variant.vcf.VCFHeader#getMetaDataInInputOrder() .
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Example 1
| Source File: StrelkaPostProcessApplication.java From hmftools with GNU General Public License v3.0 | 6 votes |
|
@NotNull
public static VCFHeader generateOutputHeader(@NotNull final VCFHeader header, @NotNull final String sampleName) {
final VCFHeader outputVCFHeader = new VCFHeader(header.getMetaDataInInputOrder(), Sets.newHashSet(sampleName));
outputVCFHeader.addMetaDataLine(VCFStandardHeaderLines.getFormatLine("GT"));
outputVCFHeader.addMetaDataLine(VCFStandardHeaderLines.getFormatLine("AD"));
outputVCFHeader.addMetaDataLine(new VCFHeaderLine("StrelkaGATKCompatibility",
"Added GT fields to strelka calls for gatk compatibility."));
outputVCFHeader.addMetaDataLine(new VCFInfoHeaderLine("MAPPABILITY", 1, VCFHeaderLineType.Float, "Mappability (percentage)"));
outputVCFHeader.addMetaDataLine(new VCFInfoHeaderLine("SOMATIC_PON_COUNT",
1,
VCFHeaderLineType.Integer,
"Number of times the variant appears in the somatic PON"));
outputVCFHeader.addMetaDataLine(new VCFInfoHeaderLine("GERMLINE_PON_COUNT",
1,
VCFHeaderLineType.Integer,
"Number of times the variant appears in the germline PON"));
return outputVCFHeader;
}
Example 2
| Source File: StructuralVariantHeader.java From hmftools with GNU General Public License v3.0 | 5 votes |
|
@NotNull
public static VCFHeader generateHeader(@NotNull final String purpleVersion, @NotNull final VCFHeader template) {
final VCFHeader outputVCFHeader = new VCFHeader(template.getMetaDataInInputOrder(), template.getGenotypeSamples());
outputVCFHeader.addMetaDataLine(new VCFHeaderLine("purpleVersion", purpleVersion));
outputVCFHeader.addMetaDataLine(VCFStandardHeaderLines.getFormatLine("GT"));
outputVCFHeader.addMetaDataLine(new VCFInfoHeaderLine(StructuralVariantFactory.RECOVERED,
0,
VCFHeaderLineType.Flag,
RECOVERED_DESC));
outputVCFHeader.addMetaDataLine(new VCFInfoHeaderLine(StructuralVariantFactory.INFERRED, 0, VCFHeaderLineType.Flag, INFERRED_DESC));
outputVCFHeader.addMetaDataLine(new VCFFilterHeaderLine(INFERRED, INFERRED_DESC));
outputVCFHeader.addMetaDataLine(new VCFInfoHeaderLine(StructuralVariantFactory.IMPRECISE,
0,
VCFHeaderLineType.Flag,
IMPRECISE_DESC));
outputVCFHeader.addMetaDataLine(new VCFInfoHeaderLine(CIPOS, 2, VCFHeaderLineType.Integer, CIPOS_DESC));
outputVCFHeader.addMetaDataLine(new VCFInfoHeaderLine(SVTYPE, 1, VCFHeaderLineType.String, SVTYPE_DESC));
outputVCFHeader.addMetaDataLine(new VCFInfoHeaderLine(PURPLE_AF_INFO, UNBOUNDED, VCFHeaderLineType.Float, PURPLE_AF_DESC));
outputVCFHeader.addMetaDataLine(new VCFInfoHeaderLine(PURPLE_CN_INFO, UNBOUNDED, VCFHeaderLineType.Float, PURPLE_CN_DESC));
outputVCFHeader.addMetaDataLine(new VCFInfoHeaderLine(RECOVERY_METHOD, 1, VCFHeaderLineType.String, RECOVERY_METHOD_DESC));
outputVCFHeader.addMetaDataLine(new VCFInfoHeaderLine(RECOVERY_FILTER, UNBOUNDED, VCFHeaderLineType.String, RECOVERY_FILTER_DESC));
outputVCFHeader.addMetaDataLine(new VCFInfoHeaderLine(PURPLE_JUNCTION_COPY_NUMBER_INFO, 1, VCFHeaderLineType.Float,
PURPLE_JUNCTION_COPY_NUMBER_DESC));
outputVCFHeader.addMetaDataLine(new VCFInfoHeaderLine(PURPLE_CN_CHANGE_INFO,
UNBOUNDED,
VCFHeaderLineType.Float,
PURPLE_CN_CHANGE_DESC));
return outputVCFHeader;
}
Example 3
| Source File: SageHotspotAnnotation.java From hmftools with GNU General Public License v3.0 | 5 votes |
|
@NotNull
private static VCFHeader generateOutputHeader(@NotNull final VCFHeader template, @NotNull final VCFHeader hotspotVCF) {
final VCFHeader outputVCFHeader = new VCFHeader(template.getMetaDataInInputOrder(), template.getGenotypeSamples());
outputVCFHeader.addMetaDataLine(new VCFInfoHeaderLine(HOTSPOT_FLAG, 0, VCFHeaderLineType.Flag, HOTSPOT_DESCRIPTION));
outputVCFHeader.addMetaDataLine(new VCFInfoHeaderLine(NEAR_HOTSPOT_FLAG, 0, VCFHeaderLineType.Flag, NEAR_HOTSPOT_DESCRIPTION));
outputVCFHeader.addMetaDataLine(new VCFInfoHeaderLine(RECOVERED_FLAG, 0, VCFHeaderLineType.Flag, RECOVERED_FLAG_DESCRIPTION));
for (VCFInfoHeaderLine headerLine : hotspotVCF.getInfoHeaderLines()) {
outputVCFHeader.addMetaDataLine(headerLine);
}
return outputVCFHeader;
}
Example 4
| Source File: RenameSampleInVcf.java From picard with MIT License | 5 votes |
|
@Override
protected int doWork() {
IOUtil.assertFileIsReadable(INPUT);
IOUtil.assertFileIsWritable(OUTPUT);
final VCFFileReader in = new VCFFileReader(INPUT, false);
final VCFHeader header = in.getFileHeader();
if (header.getGenotypeSamples().size() > 1) {
throw new IllegalArgumentException("Input VCF must be single-sample.");
}
if (OLD_SAMPLE_NAME != null && !OLD_SAMPLE_NAME.equals(header.getGenotypeSamples().get(0))) {
throw new IllegalArgumentException("Input VCF did not contain expected sample. Contained: " + header.getGenotypeSamples().get(0));
}
final EnumSet<Options> options = EnumSet.copyOf(VariantContextWriterBuilder.DEFAULT_OPTIONS);
if (CREATE_INDEX) options.add(Options.INDEX_ON_THE_FLY); else options.remove(Options.INDEX_ON_THE_FLY);
final VCFHeader outHeader = new VCFHeader(header.getMetaDataInInputOrder(), CollectionUtil.makeList(NEW_SAMPLE_NAME));
final VariantContextWriter out = new VariantContextWriterBuilder()
.setOptions(options)
.setOutputFile(OUTPUT).setReferenceDictionary(outHeader.getSequenceDictionary()).build();
out.writeHeader(outHeader);
for (final VariantContext ctx : in) {
out.add(ctx);
}
out.close();
in.close();
return 0;
}
Example 5
| Source File: LazyVCFGenotypesContext.java From Hadoop-BAM with MIT License | 5 votes |
|
@Override public void setHeader(VCFHeader header) {
VCFHeaderVersion version = null;
// Normally AbstractVCFCodec parses the header and thereby sets the
// version field. It gets used later on so we need to set it.
for (final VCFHeaderLine line : header.getMetaDataInInputOrder()) {
if (VCFHeaderVersion.isFormatString(line.getKey())) {
version = VCFHeaderVersion.toHeaderVersion(line.getValue());
break;
}
}
codec.setHeaderAndVersion(header, version);
}
Example 6
| Source File: UpdateVCFSequenceDictionary.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
|
@Override
public void onTraversalStart() {
VCFHeader inputHeader = getHeaderForVariants();
VCFHeader outputHeader = inputHeader == null ?
new VCFHeader() :
new VCFHeader(inputHeader.getMetaDataInInputOrder(), inputHeader.getGenotypeSamples()) ;
getDefaultToolVCFHeaderLines().forEach(line -> outputHeader.addMetaDataLine(line));
sourceDictionary = getBestAvailableSequenceDictionary();
// If -replace is set, do not need to check the sequence dictionary for validity here -- it will still be
// checked in our normal sequence dictionary validation. Warn and require opt-in via -replace if we're about to
// clobber a valid sequence dictionary. Check the input file directly via the header rather than using the
// engine, since it might dig one up from an index.
if (!replace) {
SAMSequenceDictionary oldDictionary =
inputHeader == null ? null : inputHeader.getSequenceDictionary();
if (oldDictionary != null && !oldDictionary.getSequences().isEmpty()) {
throw new CommandLineException.BadArgumentValue(
String.format(
"The input variant file %s already contains a sequence dictionary. " +
"Use %s to force the dictionary to be replaced.",
getDrivingVariantsFeatureInput().getName(),
REPLACE_ARGUMENT_NAME
)
);
}
}
outputHeader.setSequenceDictionary(sourceDictionary);
vcfWriter = createVCFWriter(new File(outFile));
vcfWriter.writeHeader(outputHeader);
}
Example 7
| Source File: CombineGVCFs.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
|
private VariantContextWriter getVCFWriter() {
final SortedSet<String> samples = getSamplesForVariants();
final VCFHeader inputVCFHeader = new VCFHeader(getHeaderForVariants().getMetaDataInInputOrder(), samples);
final Set<VCFHeaderLine> headerLines = new LinkedHashSet<>(inputVCFHeader.getMetaDataInInputOrder());
headerLines.addAll(getDefaultToolVCFHeaderLines());
headerLines.addAll(annotationEngine.getVCFAnnotationDescriptions());
// add headers for annotations added by this tool
headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.DEPTH_KEY)); // needed for gVCFs without DP tags
if ( dbsnp.dbsnp != null ) {
VCFStandardHeaderLines.addStandardInfoLines(headerLines, true, VCFConstants.DBSNP_KEY);
}
if (somaticInput) {
//single-sample M2 variant filter status will get moved to genotype filter
headerLines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_FILTER_KEY));
if (!dropSomaticFilteringAnnotations) {
//standard M2 INFO annotations for filtering will get moved to FORMAT field
for (final String key : Mutect2FilteringEngine.STANDARD_MUTECT_INFO_FIELDS_FOR_FILTERING) {
headerLines.add(GATKVCFHeaderLines.getEquivalentFormatHeaderLine(key));
}
}
}
VariantContextWriter writer = createVCFWriter(outputFile);
final Set<String> sampleNameSet = new IndexedSampleList(samples).asSetOfSamples();
final VCFHeader vcfHeader = new VCFHeader(headerLines, new TreeSet<>(sampleNameSet));
writer.writeHeader(vcfHeader);
return writer;
}
Example 8
| Source File: FixCallSetSampleOrdering.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
|
@Override
public void onTraversalStart() {
assertThatTheyReallyWantToProceed();
if (batchSize == 0) {
throw new SampleNameFixingCannotProceedException("your callset is not affected by the bug if you ran with --"+ GenomicsDBImport.BATCHSIZE_ARG_LONG_NAME +" 0");
}
if ( readerThreads > 1 ) {
if ( gvcfToHeaderSampleMapFile == null ) {
throw new SampleNameFixingCannotProceedException("You must provide a --gvcfToHeaderSampleMapFile if GenomicsDBImport was run with --" + GenomicsDBImport.VCF_INITIALIZER_THREADS_LONG_NAME + " > 1");
}
} else if ( gvcfToHeaderSampleMapFile != null ) {
throw new SampleNameFixingCannotProceedException("You must NOT provide a --gvcfToHeaderSampleMapFile if GenomicsDBImport was run with --" + GenomicsDBImport.VCF_INITIALIZER_THREADS_LONG_NAME + " 1");
}
final VCFHeader originalHeader = getHeaderForVariants();
final Set<VCFHeaderLine> originalHeaderLines = originalHeader.getMetaDataInInputOrder();
final Set<VCFHeaderLine> newHeaderLines = new LinkedHashSet<>(originalHeaderLines);
newHeaderLines.addAll(getDefaultToolVCFHeaderLines());
loadSampleNameMappings();
final List<String> sampleNamesOriginalOrdering = new ArrayList<>(sampleNameMapFromGenomicsDBImport.keySet());
if( sampleNamesOriginalOrdering.size() <= batchSize ){
throw new SampleNameFixingCannotProceedException("you are not affected by the sample name ordering bug if your batch size is >= the number of samples in your callset. \n"
+ "batch size: " + batchSize + "\n"
+ "number of samples: " + sampleNamesOriginalOrdering.size());
}
assertSampleNamesMatchInputVCF(originalHeader.getSampleNamesInOrder(), sampleNamesOriginalOrdering);
final List<String> batchSortedSampleNames = getBatchSortedList();
final VCFHeader remappedHeader = new VCFHeader(newHeaderLines, batchSortedSampleNames);
logger.info("Writing the new header with corrected sample names");
writer = createVCFWriter(output);
writer.writeHeader(remappedHeader);
logger.info("Copying the rest of the VCF");
}
Example 9
| Source File: AnnotateStrelkaWithAllelicDepth.java From hmftools with GNU General Public License v3.0 | 4 votes |
|
@NotNull
private VCFHeader generateOutputHeader(@NotNull final VCFHeader template) {
final VCFHeader outputVCFHeader = new VCFHeader(template.getMetaDataInInputOrder(), template.getGenotypeSamples());
outputVCFHeader.addMetaDataLine(VCFStandardHeaderLines.getFormatLine("AD"));
return outputVCFHeader;
}
Example 10
| Source File: GenomeWarpSerial.java From genomewarp with Apache License 2.0 | 4 votes |
|
private static VCFHeader warpHeader(VCFHeader in, Map<String, Long> namesAndLength)
throws IllegalArgumentException {
Set<VCFHeaderLine> newLines = new HashSet<>();
boolean hasSource = false;
VCFHeaderVersion version = DEFAULT_VCF_VERSION;
for (VCFHeaderLine line : in.getMetaDataInInputOrder()) {
if (line.getKey().equals("reference")) {
newLines.add(new VCFHeaderLine(line.getKey(), ARGS.refTargetFASTA));
} else if (line.getKey().equals("source")) {
newLines.add(new VCFHeaderLine(line.getKey(), line.getValue() + "_and_"
+ GENOME_WARP_VERSION));
hasSource = true;
} else if (line.getKey().equals("fileformat")) {
version = VCFHeaderVersion.toHeaderVersion(line.getValue());
if (version == null) {
throw new IllegalArgumentException("malformed version: " + line.getValue());
}
} else if (line.getKey().equals(VCFConstants.CONTIG_HEADER_KEY)) {
continue;
} else {
newLines.add(line);
}
}
if (!hasSource) {
newLines.add(new VCFHeaderLine("source", GENOME_WARP_VERSION));
}
// Add contigs
int i = 0;
for (Map.Entry<String, Long> entry : namesAndLength.entrySet()) {
String currName = entry.getKey();
long chrSize = entry.getValue();
newLines.add(new VCFContigHeaderLine(VCFHeaderLine.toStringEncoding(
createContigEntry(currName, chrSize, ARGS.targetAssembly, ARGS.species)),
version, VCFConstants.CONTIG_HEADER_KEY, i++));
}
return new VCFHeader(newLines, in.getSampleNamesInOrder());
}
Example 11
| Source File: MakeSitesOnlyVcf.java From picard with MIT License | 4 votes |
|
@Override
protected int doWork() {
IOUtil.assertFileIsReadable(INPUT);
IOUtil.assertFileIsWritable(OUTPUT);
final VCFFileReader reader = new VCFFileReader(INPUT, false);
final VCFHeader inputVcfHeader = new VCFHeader(reader.getFileHeader().getMetaDataInInputOrder());
final SAMSequenceDictionary sequenceDictionary = inputVcfHeader.getSequenceDictionary();
if (CREATE_INDEX && sequenceDictionary == null) {
throw new PicardException("A sequence dictionary must be available (either through the input file or by setting it explicitly) when creating indexed output.");
}
final ProgressLogger progress = new ProgressLogger(Log.getInstance(MakeSitesOnlyVcf.class), 10000);
// Setup the site-only file writer
final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
.setOutputFile(OUTPUT)
.setReferenceDictionary(sequenceDictionary);
if (CREATE_INDEX)
builder.setOption(Options.INDEX_ON_THE_FLY);
else
builder.unsetOption(Options.INDEX_ON_THE_FLY);
final VariantContextWriter writer = builder.build();
final VCFHeader header = new VCFHeader(inputVcfHeader.getMetaDataInInputOrder(), SAMPLE);
writer.writeHeader(header);
// Go through the input, strip the records and write them to the output
final CloseableIterator<VariantContext> iterator = reader.iterator();
while (iterator.hasNext()) {
final VariantContext full = iterator.next();
final VariantContext site = subsetToSamplesWithOriginalAnnotations(full, SAMPLE);
writer.add(site);
progress.record(site.getContig(), site.getStart());
}
CloserUtil.close(iterator);
CloserUtil.close(reader);
writer.close();
return 0;
}
Example 12
| Source File: GnarlyGenotyper.java From gatk with BSD 3-Clause "New" or "Revised" License | 4 votes |
|
private void setupVCFWriter(VCFHeader inputVCFHeader, SampleList samples) {
final Set<VCFHeaderLine> headerLines = new LinkedHashSet<>(inputVCFHeader.getMetaDataInInputOrder());
headerLines.addAll(getDefaultToolVCFHeaderLines());
// Remove GCVFBlocks
headerLines.removeIf(vcfHeaderLine -> vcfHeaderLine.getKey().startsWith(GVCFWriter.GVCF_BLOCK));
//add header for new filter
headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.LOW_QUAL_FILTER_NAME));
// add headers for annotations added by this tool
headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY));
headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_FREQUENCY_KEY));
headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY));
headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AC_ADJUSTED_KEY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.FISHER_STRAND_KEY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.STRAND_ODDS_RATIO_KEY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.SB_TABLE_KEY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.EXCESS_HET_KEY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.QUAL_BY_DEPTH_KEY));
headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.RMS_MAPPING_QUALITY_KEY));
headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.DEPTH_KEY)); // needed for gVCFs without DP tags
if (inputVCFHeader.hasInfoLine(GATKVCFConstants.AS_QUAL_KEY) || inputVCFHeader.hasInfoLine(GATKVCFConstants.AS_RAW_QUAL_APPROX_KEY)) { //use this as a proxy for all AS headers
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_ALT_ALLELE_DEPTH_KEY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_BASE_QUAL_RANK_SUM_KEY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_FISHER_STRAND_KEY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_RMS_MAPPING_QUALITY_KEY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_MAP_QUAL_RANK_SUM_KEY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_QUAL_BY_DEPTH_KEY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_READ_POS_RANK_SUM_KEY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_STRAND_ODDS_RATIO_KEY));
}
if ( dbsnp.dbsnp != null ) {
VCFStandardHeaderLines.addStandardInfoLines(headerLines, true, VCFConstants.DBSNP_KEY);
}
vcfWriter = createVCFWriter(outputFile);
if (outputDbName != null) {
annotationDatabaseWriter = createVCFWriter(new File(outputDbName));
}
final Set<String> sampleNameSet = samples.asSetOfSamples();
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.RAW_GENOTYPE_COUNT_KEY));
if (SUMMARIZE_PLs) {
headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.REFERENCE_GENOTYPE_QUALITY));
headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.GENOTYPE_QUALITY_BY_ALLELE_BALANCE));
headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.GENOTYPE_QUALITY_BY_ALT_CONFIDENCE));
}
final VCFHeader vcfHeader = new VCFHeader(headerLines, new TreeSet<>(sampleNameSet));
final VCFHeader dbHeader = new VCFHeader(headerLines);
vcfWriter.writeHeader(vcfHeader);
if (outputDbName != null) {
annotationDatabaseWriter.writeHeader(dbHeader);
}
}
