Package htsjdk.variant.variantcontext.writer

Examples of htsjdk.variant.variantcontext.writer.VariantContextWriter

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        final List<VariantFilter>  variantFilters = CollectionUtil.makeList(new AlleleBalanceFilter(MIN_AB), new FisherStrandFilter(MAX_FS), new QdFilter(MIN_QD));
        final List<GenotypeFilter> genotypeFilters = CollectionUtil.makeList(new GenotypeQualityFilter(MIN_GQ), new DepthFilter(MIN_DP));
        final VCFFileReader in = new VCFFileReader(INPUT, false);
        final FilterApplyingVariantIterator iterator = new FilterApplyingVariantIterator(in.iterator(), variantFilters, genotypeFilters);

        final VariantContextWriter out = new VariantContextWriterBuilder().setOutputFile(OUTPUT).build();
        final VCFHeader header = in.getFileHeader();
        header.addMetaDataLine(new VCFFilterHeaderLine("AllGtsFiltered", "Site filtered out because all genotypes are filtered out."));
        header.addMetaDataLine(new VCFFormatHeaderLine("FT", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Genotype filters."));
        for (final VariantFilter filter : variantFilters) {
            for (final VCFFilterHeaderLine line : filter.headerLines()) {
                header.addMetaDataLine(line);
            }
        }

        out.writeHeader(in.getFileHeader());

        while (iterator.hasNext()) {
            out.add(iterator.next());
        }

        out.close();
        in.close();
        return 0;
    }
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                .setReferenceDictionary(sequenceDictionary)
                .clearOptions();
        if (CREATE_INDEX)
            builder.setOption(Options.INDEX_ON_THE_FLY);

    final VariantContextWriter snpWriter = builder.setOutputFile(SNP_OUTPUT).build();
    final VariantContextWriter indelWriter = builder.setOutputFile(INDEL_OUTPUT).build();
    snpWriter.writeHeader(fileHeader);
    indelWriter.writeHeader(fileHeader);

        int incorrectVariantCount = 0;

    final CloseableIterator<VariantContext> iterator = fileReader.iterator();
    while (iterator.hasNext()) {
      final VariantContext context = iterator.next();
      if (context.isIndel()) indelWriter.add(context);
      else if (context.isSNP()) snpWriter.add(context);
      else {
                if (STRICT) throw new IllegalStateException("Found a record with type " + context.getType().name());
                else incorrectVariantCount++;
            }

            progress.record(context.getChr(), context.getStart());
    }

        if (incorrectVariantCount > 0) {
            log.debug("Found " + incorrectVariantCount + " records that didn't match SNP or INDEL");
        }

    CloserUtil.close(iterator);
    CloserUtil.close(fileReader);
    snpWriter.close();
    indelWriter.close();

    return 0;
  }
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    }

    private void writeSortedOutput(final VCFHeader outputHeader, final SortingCollection<VariantContext> sortedOutput) {
        final ProgressLogger writeProgress = new ProgressLogger(log, 25000, "wrote", "records");
        final EnumSet<Options> options = CREATE_INDEX ? EnumSet.of(Options.INDEX_ON_THE_FLY) : EnumSet.noneOf(Options.class);
        final VariantContextWriter out = new VariantContextWriterBuilder().
                setReferenceDictionary(outputHeader.getSequenceDictionary()).
                setOptions(options).
                setOutputFile(OUTPUT).build();
        out.writeHeader(outputHeader);
        for (final VariantContext variantContext : sortedOutput) {
            out.add(variantContext);
            writeProgress.record(variantContext.getChr(), variantContext.getStart());
        }
        out.close();
    }
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                .setOutputFile(OUTPUT)
                .setReferenceDictionary(sequenceDictionary)
                .clearOptions();
        if (CREATE_INDEX)
            builder.setOption(Options.INDEX_ON_THE_FLY);
        final VariantContextWriter writer = builder.build();

    writer.writeHeader(new VCFHeader(VCFUtils.smartMergeHeaders(headers, false), sampleList));

    final MergingIterator<VariantContext> mergingIterator = new MergingIterator<VariantContext>(variantContextComparator, iteratorCollection);
    while (mergingIterator.hasNext()) {
      final VariantContext context = mergingIterator.next();
      writer.add(context);
      progress.record(context.getChr(), context.getStart());
    }

    CloserUtil.close(mergingIterator);
    writer.close();
    return 0;
  }
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                .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();
        writer.writeHeader(header);
      final CloseableIterator<VariantContext> iterator = reader.iterator();

      while (iterator.hasNext()) {
        final VariantContext context = iterator.next();
            writer.add(context);
            progress.record(context.getChr(), context.getStart());
        }

      CloserUtil.close(iterator);
      CloserUtil.close(reader);
        writer.close();

        return 0;
    }
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                .setReferenceDictionary(samSequenceDictionary)
                .clearOptions();
        if (CREATE_INDEX)
            builder.setOption(Options.INDEX_ON_THE_FLY);

        final VariantContextWriter vcfWriter = builder.setOutputFile(OUTPUT).build();
        fileHeader.setSequenceDictionary(samSequenceDictionary);
        vcfWriter.writeHeader(fileHeader);

        final ProgressLogger progress = new ProgressLogger(log, 10000);
        final CloseableIterator<VariantContext> iterator = fileReader.iterator();
        while (iterator.hasNext()) {
            final VariantContext context = iterator.next();
            vcfWriter.add(context);
            progress.record(context.getChr(), context.getStart());
        }

        CloserUtil.close(iterator);
        CloserUtil.close(fileReader);
        vcfWriter.close();

        return 0;
    }
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Related Classes of htsjdk.variant.variantcontext.writer.VariantContextWriter

  • org.broad.igv.cli_plugin.VCFEncoder
  • org.broad.igv.variant.vcf.VCFWriterTest
  • org.broadinstitute.gatk.engine.io.storage.VariantContextWriterStorage
  • org.broadinstitute.gatk.tools.CatVariants
  • org.broadinstitute.gatk.tools.walkers.phasing.ReadBackedPhasing
  • picard.vcf.filter.FilterVcf
  • picard.vcf.GatherVcfs
  • picard.vcf.MakeSitesOnlyVcf
  • picard.vcf.MergeVcfs
  • picard.vcf.RenameSampleInVcf
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