Package htsjdk.variant.variantcontext.writer

Examples of htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
        final SAMSequenceDictionary samSequenceDictionary = SAMSequenceDictionaryExtractor.extractDictionary(SEQUENCE_DICTIONARY);

        final VCFFileReader fileReader = new VCFFileReader(INPUT, false);
        final VCFHeader fileHeader = fileReader.getFileHeader();

        final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
                .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();
View Full Code Here
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
      }

        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
View Full Code Here
92
93
94
95
96
97
98
99
100
101
102
        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()) {
View Full Code Here
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
            : fileHeader.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 VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
                .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;
View Full Code Here
162
163
164
165
166
167
168
169
170
171
172
    }

    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) {
View Full Code Here
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
    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 VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
                .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()) {
View Full Code Here
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
      final SAMSequenceDictionary sequenceDictionary = header.getSequenceDictionary();
      if (CREATE_INDEX && sequenceDictionary == null) {
        throw new PicardException("A sequence dictionary must be available in the input file when creating indexed output.");
      }

        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();
        writer.writeHeader(header);
      final CloseableIterator<VariantContext> iterator = reader.iterator();

      while (iterator.hasNext()) {
        final VariantContext context = iterator.next();
View Full Code Here
TOP

Related Classes of htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

  • picard.vcf.filter.FilterVcf
  • picard.vcf.MakeSitesOnlyVcf
  • picard.vcf.MergeVcfs
  • picard.vcf.SortVcf
  • picard.vcf.SplitVcfs
  • picard.vcf.UpdateVcfSequenceDictionary
  • picard.vcf.VcfFormatConverter
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.