Package htsjdk.samtools

Examples of htsjdk.samtools.SAMSequenceDictionary

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    @BeforeClass
    public void init() throws FileNotFoundException {
        SAMFileReader reader = new SAMFileReader(bamFile);
        SAMSequenceDictionary sequenceDictionary = reader.getFileHeader().getSequenceDictionary();
        reader.close();
       
        bamIndex = new GATKBAMIndex(bamIndexFile);
    }
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        final PeekableIterator<SAMRecord> iterator = new PeekableIterator<SAMRecord>(sam.iterator());
        final ReferenceSequenceFile referenceFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(REFERENCE_SEQUENCE);

        {
            // Check that the sequence dictionaries match if present
            final SAMSequenceDictionary referenceDictionary= referenceFile.getSequenceDictionary();
            final SAMSequenceDictionary samFileDictionary = sam.getFileHeader().getSequenceDictionary();
            if (referenceDictionary != null && samFileDictionary != null) {
                SequenceUtil.assertSequenceDictionariesEqual(referenceDictionary, samFileDictionary);
            }
        }
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        final IntervalList originalTargets =  IntervalList.fromFile(TARGETS);

        {
            // Apply padding
            final IntervalList padded = new IntervalList(originalTargets.getHeader());
            final SAMSequenceDictionary dict = padded.getHeader().getSequenceDictionary();
            for (final Interval i : originalTargets.getIntervals()) {
                padded.add(new Interval(i.getSequence(),
                        Math.max(i.getStart() - PADDING, 1),
                        Math.min(i.getEnd() + PADDING, dict.getSequence(i.getSequence()).getSequenceLength()),
                        i.isNegativeStrand(),
                        i.getName()));
            }

            log.info("Starting with " + padded.size() + " targets.");
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        IOUtil.assertFileIsWritable(OUTPUT);

        final SAMFileReader in = new SAMFileReader(INPUT);

        ReferenceSequenceFile reference = ReferenceSequenceFileFactory.getReferenceSequenceFile(REFERENCE);
        SAMSequenceDictionary refDict = reference.getSequenceDictionary();

        if (refDict == null) {
          log.error("No reference sequence dictionary found. Aborting.  You can create a sequence dictionary for the reference fasta using CreateSequenceDictionary.jar.");
          in.close();
          return 1;
        }

        printDictionary("SAM/BAM file", in.getFileHeader().getSequenceDictionary());
        printDictionary("Reference", refDict);
        Map<Integer, Integer> newOrder = buildSequenceDictionaryMap(refDict, in.getFileHeader().getSequenceDictionary());

        // has to be after we create the newOrder
        SAMFileHeader outHeader = in.getFileHeader().clone();
        outHeader.setSequenceDictionary(refDict);

        log.info("Writing reads...");
        if (in.hasIndex()) {
            final SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(outHeader, true, OUTPUT);

            // write the reads in contig order
            for (final SAMSequenceRecord contig : refDict.getSequences() ) {
                final SAMRecordIterator it = in.query(contig.getSequenceName(), 0, 0, false);
                writeReads(out, it, newOrder, contig.getSequenceName());
            }
            // don't forget the unmapped reads
            writeReads( out, in.queryUnmapped(), newOrder, "unmapped" );
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    protected int doWork() {
        if (OUTPUT.exists()) {
            throw new PicardException(OUTPUT.getAbsolutePath() +
                    " already exists.  Delete this file and try again, or specify a different output file.");
        }
        final SAMSequenceDictionary sequences = makeSequenceDictionary(REFERENCE);
        final SAMFileHeader samHeader = new SAMFileHeader();
        samHeader.setSequenceDictionary(sequences);
        final SAMFileWriter samWriter = new SAMFileWriterFactory().makeSAMWriter(samHeader, false, OUTPUT);
        samWriter.close();
        return 0;
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                throw new PicardException("Sequence name appears more than once in reference: " + refSeq.getName());
            }
            sequenceNames.add(refSeq.getName());
            ret.add(makeSequenceRecord(refSeq));
        }
        return new SAMSequenceDictionary(ret);
    }
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        log.info("Checking inputs.");
        INPUT = IOUtil.unrollFiles(INPUT, IOUtil.VCF_EXTENSIONS);
        for (final File f: INPUT) IOUtil.assertFileIsReadable(f);
        IOUtil.assertFileIsWritable(OUTPUT);

    final SAMSequenceDictionary sequenceDictionary = VCFFileReader.getSequenceDictionary(INPUT.get(0));

        if (CREATE_INDEX && sequenceDictionary == null) {
            throw new PicardException("In order to index the resulting VCF input VCFs must contain ##contig lines.");
        }
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    }

    /** Validates that all headers contain the same set of genotyped samples and that files are in order by position of first record. */
    private static void assertSameSamplesAndValidOrdering(final List<File> inputFiles) {
        final VCFHeader header = new VCFFileReader(inputFiles.get(0), false).getFileHeader();
        final SAMSequenceDictionary dict = header.getSequenceDictionary();
        final VariantContextComparator comparator = new VariantContextComparator(header.getSequenceDictionary());
        final List<String> samples = header.getGenotypeSamples();

        File lastFile = null;
        VariantContext lastContext = null;

        for (final File f : inputFiles) {
            final VCFFileReader in = new VCFFileReader(f, false);
            dict.assertSameDictionary(in.getFileHeader().getSequenceDictionary());
            final List<String> theseSamples = in.getFileHeader().getGenotypeSamples();

            if (!samples.equals(theseSamples)) {
                final SortedSet<String> s1 = new TreeSet<String>(samples);
                final SortedSet<String> s2 = new TreeSet<String>(theseSamples);
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        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.");
      }
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        IOUtil.assertFileIsWritable(detailedMetricsFile);
        IOUtil.assertFileIsWritable(contingencyMetricsFile);

        final boolean usingIntervals = this.INTERVALS != null && this.INTERVALS.size() > 0;
        IntervalList intervals = null;
        SAMSequenceDictionary intervalsSamSequenceDictionary = null;
        if (usingIntervals) {
            log.info("Loading up region lists.");
            long genomeBaseCount = 0;
            for (final File f : INTERVALS) {
                IOUtil.assertFileIsReadable(f);
                final IntervalList tmpIntervalList = IntervalList.fromFile(f);
                if (genomeBaseCount == 0) {         // Don't count the reference length more than once.
                    intervalsSamSequenceDictionary = tmpIntervalList.getHeader().getSequenceDictionary();
                    genomeBaseCount = intervalsSamSequenceDictionary.getReferenceLength();
                }

                if (intervals == null)        intervals = tmpIntervalList;
                else if (INTERSECT_INTERVALS) intervals = IntervalList.intersection(intervals, tmpIntervalList);
                else intervals =              IntervalList.union(intervals, tmpIntervalList);
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Related Classes of htsjdk.samtools.SAMSequenceDictionary

  • org.broad.igv.cli_plugin.VCFEncoder
  • org.broad.igv.plugin.mongovariant.VariantReviewSource
  • org.broad.igv.variant.vcf.VCFWriterTest
  • org.broadinstitute.gatk.engine.alignment.bwa.BWTFiles
  • org.broadinstitute.gatk.engine.alignment.reference.bwt.BWTSupplementaryFileGenerator
  • org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndexUnitTest
  • org.broadinstitute.gatk.engine.GenomeAnalysisEngine
  • org.broadinstitute.gatk.engine.iterators.VerifyingSamIteratorUnitTest
  • org.broadinstitute.gatk.engine.refdata.tracks.IndexDictionaryUtils
  • org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder
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