Package htsjdk.samtools

Examples of htsjdk.samtools.SAMFileHeader

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        final LiftOver liftOver = new LiftOver(CHAIN);
        liftOver.setLiftOverMinMatch(MIN_LIFTOVER_PCT);

        final IntervalList fromIntervals = IntervalList.fromFile(INPUT);
        final SAMFileHeader toHeader = new SAMFileReader(SEQUENCE_DICTIONARY).getFileHeader();
        liftOver.validateToSequences(toHeader.getSequenceDictionary());
        final IntervalList toIntervals = new IntervalList(toHeader);
        boolean anyFailed = false;
        for (final Interval fromInterval : fromIntervals) {
            final Interval toInterval = liftOver.liftOver(fromInterval);
            if (toInterval != null) {
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        }
        return ret;
    }

    private boolean compareHeaders() {
        final SAMFileHeader h1 = samReaders[0].getFileHeader();
        final SAMFileHeader h2 = samReaders[1].getFileHeader();
        boolean ret = compareValues(h1.getVersion(), h2.getVersion(), "File format version");
        ret = compareValues(h1.getCreator(), h2.getCreator(), "File creator") && ret;
        ret = compareValues(h1.getAttribute("SO"), h2.getAttribute("SO"), "Sort order") && ret;
        if (!compareSequenceDictionaries(h1, h2)) {
            ret = false;
            sequenceDictionariesDiffer = true;
        }
        ret = compareReadGroups(h1, h2) && ret;
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    private void filterReads(final FilteringIterator filteringIterator) {

        // get OUTPUT header from INPUT and owerwrite it if necessary
        final SAMFileReader inputReader = new SAMFileReader(INPUT);
        final SAMFileHeader.SortOrder inputSortOrder = inputReader.getFileHeader().getSortOrder();
        final SAMFileHeader outputHeader = inputReader.getFileHeader();
        if (SORT_ORDER != null) {
            outputHeader.setSortOrder(SORT_ORDER);
        }
        final boolean presorted = inputSortOrder.equals(outputHeader.getSortOrder());
        log.info("Filtering [presorted=" + presorted + "] " + INPUT.getName() + " -> OUTPUT=" +
            OUTPUT.getName() + " [sortorder=" + outputHeader.getSortOrder().name() + "]");

        // create OUTPUT file
        final SAMFileWriter outputWriter = new SAMFileWriterFactory().makeSAMOrBAMWriter(outputHeader, presorted, OUTPUT);

        final ProgressLogger progress = new ProgressLogger(log, (int) 1e6, "Written");
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            mergingSamRecordIteratorAssumeSorted = false;
            presorted = false;
        }
        final SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(headerMergerSortOrder, headers, MERGE_SEQUENCE_DICTIONARIES);
        final MergingSamRecordIterator iterator = new MergingSamRecordIterator(headerMerger, readers, mergingSamRecordIteratorAssumeSorted);
        final SAMFileHeader header = headerMerger.getMergedHeader();
        for (final String comment : COMMENT) {
            header.addComment(comment);
        }
        header.setSortOrder(SORT_ORDER);
        final SAMFileWriterFactory samFileWriterFactory = new SAMFileWriterFactory();
        if (USE_THREADING) {
            samFileWriterFactory.setUseAsyncIo(true);
        }
        final SAMFileWriter out = samFileWriterFactory.makeSAMOrBAMWriter(header, presorted, OUTPUT);
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        final SAMRecord firstUnmappedRec = unmappedSamFileIterator.next();
        final SAMRecord secondUnmappedRec = unmappedSamFileIterator.next();
        unmappedSamFileIterator.close();
        final File alignedSam = File.createTempFile("aligned.", ".sam");
        alignedSam.deleteOnExit();
        final SAMFileHeader alignedHeader = new SAMFileHeader();
        alignedHeader.setSortOrder(SAMFileHeader.SortOrder.queryname);
        alignedHeader.setSequenceDictionary(new SAMFileReader(sequenceDict).getFileHeader().getSequenceDictionary());
        final SAMFileWriter alignedWriter = new SAMFileWriterFactory().makeSAMWriter(alignedHeader, true, alignedSam);
        for (int i = 0; i < Math.max(firstOfPair.size(), secondOfPair.size()); ++i) {
            final HitSpec firstHitSpec = firstOfPair.isEmpty()? null: firstOfPair.get(i);
            final HitSpec secondHitSpec = secondOfPair.isEmpty()? null: secondOfPair.get(i);
            final SAMRecord first = makeRead(alignedHeader, firstUnmappedRec, firstHitSpec, true, i);
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        final SAMRecordIterator unmappedSamFileIterator = new SAMFileReader(unmappedSam).iterator();
        final SAMRecord unmappedRec = unmappedSamFileIterator.next();
        unmappedSamFileIterator.close();
        final File alignedSam = File.createTempFile("aligned.", ".sam");
        alignedSam.deleteOnExit();
        final SAMFileHeader alignedHeader = new SAMFileHeader();
        alignedHeader.setSortOrder(SAMFileHeader.SortOrder.queryname);
        alignedHeader.setSequenceDictionary(new SAMFileReader(sequenceDict).getFileHeader().getSequenceDictionary());
        final SAMFileWriter alignedWriter = new SAMFileWriterFactory().makeSAMWriter(alignedHeader, true, alignedSam);
        for (int i = 0; i < hitSpecs.size(); ++i) {
            final HitSpec hitSpec = hitSpecs.get(i);
            final SAMRecord mappedRec = makeRead(alignedHeader, unmappedRec, hitSpec, i);
            if (mappedRec != null) {
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        output.deleteOnExit();

        final File unmappedSam = File.createTempFile("unmapped.", ".sam");
        unmappedSam.deleteOnExit();
        final SAMFileWriterFactory factory = new SAMFileWriterFactory();
        final SAMFileHeader header = new SAMFileHeader();
        header.setSortOrder(SAMFileHeader.SortOrder.queryname);
        final String cigar = "16M";

        final SAMRecord firstOfPair = new SAMRecord(header);
        firstOfPair.setReadName("theRead");
        firstOfPair.setReadString("ACGTACGTACGTACGT");
        firstOfPair.setBaseQualityString("5555555555555555");
        firstOfPair.setReadUnmappedFlag(true);
        firstOfPair.setReadPairedFlag(true);
        firstOfPair.setFirstOfPairFlag(true);

        final SAMRecord secondOfPair = new SAMRecord(header);
        secondOfPair.setReadName("theRead");
        secondOfPair.setReadString("ACGTACGTACGTACGT");
        secondOfPair.setBaseQualityString("5555555555555555");
        secondOfPair.setReadUnmappedFlag(true);
        secondOfPair.setReadPairedFlag(true);
        secondOfPair.setSecondOfPairFlag(true);
        SamPairUtil.setMateInfo(firstOfPair, secondOfPair, header);

        final SAMFileWriter unmappedWriter = factory.makeSAMWriter(header, false, unmappedSam);
        unmappedWriter.addAlignment(firstOfPair);
        unmappedWriter.addAlignment(secondOfPair);
        unmappedWriter.close();

        final File alignedSam = File.createTempFile("aligned.", ".sam");
        alignedSam.deleteOnExit();

        // Populate the header with SAMSequenceRecords
        header.getSequenceDictionary().addSequence(new SAMSequenceRecord("chr1", 1000000));

        // Create 2 alignments for each end of pair
        final SAMFileWriter alignedWriter = factory.makeSAMWriter(header, false, alignedSam);
        for (int i = 1; i <= 2; ++i) {
            final SAMRecord firstOfPairAligned = new SAMRecord(header);
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    private File[] createSamFilesToBeMerged(final MultipleAlignmentSpec[] specs) {
        try {
            final File unmappedSam = File.createTempFile("unmapped.", ".sam");
            unmappedSam.deleteOnExit();
            final SAMFileWriterFactory factory = new SAMFileWriterFactory();
            final SAMFileHeader header = new SAMFileHeader();
            header.setSortOrder(SAMFileHeader.SortOrder.queryname);
            final SAMRecord unmappedRecord = new SAMRecord(header);

            unmappedRecord.setReadName("theRead");
            unmappedRecord.setReadString("ACGTACGTACGTACGT");
            unmappedRecord.setBaseQualityString("5555555555555555");
            unmappedRecord.setReadUnmappedFlag(true);

            final SAMFileWriter unmappedWriter = factory.makeSAMWriter(header, false, unmappedSam);
            unmappedWriter.addAlignment(unmappedRecord);
            unmappedWriter.close();

            final File alignedSam = File.createTempFile("aligned.", ".sam");
            alignedSam.deleteOnExit();

            final String sequence = "chr1";
            // Populate the header with SAMSequenceRecords
            header.getSequenceDictionary().addSequence(new SAMSequenceRecord(sequence, 1000000));

            final SAMFileWriter alignedWriter = factory.makeSAMWriter(header, false, alignedSam);
            for (final MultipleAlignmentSpec spec : specs) {
                final SAMRecord alignedRecord = new SAMRecord(header);
                alignedRecord.setReadName(unmappedRecord.getReadName());
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                                              final boolean includeSecondary, final int expectedFirstMapq,
                                              final int expectedSecondMapq) throws Exception {
        final File unmappedSam = File.createTempFile("unmapped.", ".sam");
        unmappedSam.deleteOnExit();
        final SAMFileWriterFactory factory = new SAMFileWriterFactory();
        final SAMFileHeader header = new SAMFileHeader();
        header.setSortOrder(SAMFileHeader.SortOrder.queryname);

        final String readName = "theRead";
        final SAMRecord firstUnmappedRead = new SAMRecord(header);
        firstUnmappedRead.setReadName(readName);
        firstUnmappedRead.setReadString("ACGTACGTACGTACGT");
        firstUnmappedRead.setBaseQualityString("5555555555555555");
        firstUnmappedRead.setReadUnmappedFlag(true);
        firstUnmappedRead.setMateUnmappedFlag(true);
        firstUnmappedRead.setReadPairedFlag(true);
        firstUnmappedRead.setFirstOfPairFlag(true);

        final SAMRecord secondUnmappedRead = new SAMRecord(header);
        secondUnmappedRead.setReadName(readName);
        secondUnmappedRead.setReadString("TCGAACGTTCGAACTG");
        secondUnmappedRead.setBaseQualityString("6666666666666666");
        secondUnmappedRead.setReadUnmappedFlag(true);
        secondUnmappedRead.setMateUnmappedFlag(true);
        secondUnmappedRead.setReadPairedFlag(true);
        secondUnmappedRead.setSecondOfPairFlag(true);



        final SAMFileWriter unmappedWriter = factory.makeSAMWriter(header, false, unmappedSam);
        unmappedWriter.addAlignment(firstUnmappedRead);
        unmappedWriter.addAlignment(secondUnmappedRead);
        unmappedWriter.close();

        final File alignedSam = File.createTempFile("aligned.", ".sam");
        alignedSam.deleteOnExit();

        final String sequence = "chr1";
        // Populate the header with SAMSequenceRecords
        header.getSequenceDictionary().addSequence(new SAMSequenceRecord(sequence, 1000000));

        final SAMFileWriter alignedWriter = factory.makeSAMWriter(header, false, alignedSam);

        addAlignmentsForBestFragmentMapqStrategy(alignedWriter, firstUnmappedRead, sequence, firstMapQs);
        addAlignmentsForBestFragmentMapqStrategy(alignedWriter, secondUnmappedRead, sequence, secondMapQs);
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        final MostDistantStrategyAlignmentSpec[] secondEndSpecs) throws Exception {

        final File unmappedSam = File.createTempFile("unmapped.", ".sam");
        unmappedSam.deleteOnExit();
        final SAMFileWriterFactory factory = new SAMFileWriterFactory();
        final SAMFileHeader header = new SAMFileHeader();
        header.setSortOrder(SAMFileHeader.SortOrder.queryname);

        final String readName = "theRead";
        final SAMRecord firstUnmappedRead = new SAMRecord(header);
        firstUnmappedRead.setReadName(readName);
        firstUnmappedRead.setReadString("ACGT");
        firstUnmappedRead.setBaseQualityString("5555");
        firstUnmappedRead.setReadUnmappedFlag(true);
        firstUnmappedRead.setMateUnmappedFlag(true);
        firstUnmappedRead.setReadPairedFlag(true);
        firstUnmappedRead.setFirstOfPairFlag(true);

        final SAMRecord secondUnmappedRead = new SAMRecord(header);
        secondUnmappedRead.setReadName(readName);
        secondUnmappedRead.setReadString("TCGA");
        secondUnmappedRead.setBaseQualityString("6666");
        secondUnmappedRead.setReadUnmappedFlag(true);
        secondUnmappedRead.setMateUnmappedFlag(true);
        secondUnmappedRead.setReadPairedFlag(true);
        secondUnmappedRead.setSecondOfPairFlag(true);



        final SAMFileWriter unmappedWriter = factory.makeSAMWriter(header, false, unmappedSam);
        unmappedWriter.addAlignment(firstUnmappedRead);
        unmappedWriter.addAlignment(secondUnmappedRead);
        unmappedWriter.close();

        final File alignedSam = File.createTempFile("aligned.", ".sam");
        alignedSam.deleteOnExit();

        final SAMFileReader dictReader = new SAMFileReader(sequenceDict);
        header.setSequenceDictionary(dictReader.getFileHeader().getSequenceDictionary());
        dictReader.close();

        final SAMFileWriter alignedWriter = factory.makeSAMWriter(header, false, alignedSam);

        String expectedFirstPrimarySequence = null;
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Related Classes of htsjdk.samtools.SAMFileHeader

  • org.broad.igv.sam.PicardAlignment
  • org.broad.igv.sam.reader.BAMFileReader
  • org.broad.igv.sam.reader.BAMHttpQueryReaderTest
  • org.broad.igv.sam.reader.BAMHttpReader
  • org.broad.igv.sam.reader.MergedAlignmentReader
  • org.broad.igv.sam.reader.SAMFileGroup
  • org.broadinstitute.gatk.engine.datasources.reads.ActiveRegionShardBalancerUnitTest
  • org.broadinstitute.gatk.engine.downsampling.AlleleBiasedDownsamplingUtilsUnitTest
  • org.broadinstitute.gatk.engine.downsampling.DownsamplingReadsIteratorUnitTest
  • org.broadinstitute.gatk.engine.downsampling.FractionalDownsamplerUnitTest$FractionalDownsamplerTest
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