Package htsjdk.samtools

Examples of htsjdk.samtools.SAMRecordIterator

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    public boolean hasIndex() {
        return reader.hasIndex();
    }

    public CloseableIterator<PicardAlignment> query(String sequence, int start, int end, boolean contained) {
        SAMRecordIterator query = null;
        try {
            query = reader.query(sequence, start + 1, end, contained);
            return new WrappedIterator(query);
        } catch (ArrayIndexOutOfBoundsException e) {
            log.error("Error querying BAM file ", e);
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        assertEquals("Index file existence unexpected: " + indexFile.getAbsolutePath(), createIndex, indexFile.exists());

        SAMFileReader writtenReader = new SAMFileReader(new File(outPath));
        writtenReader.setValidationStringency(ValidationStringency.SILENT);
        SAMRecordIterator iter = null;
        if(createIndex){
            iter = writtenReader.queryOverlapping(sequence, start + 1, end);
        }else{
            iter = writtenReader.iterator();
        }

        int readCount = 0;
        while (iter.hasNext()) {
            readCount++;
            iter.next();
        }

        System.out.println(readCount + " alignments read");
        assertTrue("No alignments read", readCount > 0);
        assertEquals("Read a different number of alignments than written", writtenCount, readCount);
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    public DiffElement readFromFile(File file, int maxElementsToRead) {
        final SAMFileReader reader = new SAMFileReader(file, null); // null because we don't want it to look for the index
        reader.setValidationStringency(ValidationStringency.SILENT);

        DiffNode root = DiffNode.rooted(file.getName());
        SAMRecordIterator iterator = reader.iterator();

        int count = 0;
        while ( iterator.hasNext() ) {
            final SAMRecord record = iterator.next();

            // name is the read name + first of pair
            String name = record.getReadName().replace('.', '_');
            if ( record.getReadPairedFlag() ) {
                name += record.getFirstOfPairFlag() ? "_1" : "_2";
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        final GenomeLocParser genomeLocParser = new GenomeLocParser(reference);

        final SAMFileReader reader = new SAMFileReader(samFile);
        reader.setSAMRecordFactory(new GATKSamRecordFactory());

        SAMRecordIterator rawIterator;
        if ( location == null )
            rawIterator = reader.iterator();
        else {
            final GenomeLoc loc = genomeLocParser.parseGenomeLoc(location);
            rawIterator = reader.query(loc.getContig(), loc.getStart(), loc.getStop(), false);
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        ////////////////////////////////////////////////////////////////////////
        // Main loop that consumes reads, clips them and writes them to the output
        ////////////////////////////////////////////////////////////////////////
        final ProgressLogger progress = new ProgressLogger(log, 1000000, "Read");
        final SAMRecordIterator iterator = in.iterator();

        final AdapterMarker adapterMarker = new AdapterMarker(ADAPTER_TRUNCATION_LENGTH, adapters).
                setMaxPairErrorRate(MAX_ERROR_RATE_PE).setMinPairMatchBases(MIN_MATCH_BASES_PE).
                setMaxSingleEndErrorRate(MAX_ERROR_RATE_SE).setMinSingleEndMatchBases(MIN_MATCH_BASES_SE).
                setNumAdaptersToKeep(NUM_ADAPTERS_TO_KEEP).
                setThresholdForSelectingAdaptersToKeep(PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN);

        while (iterator.hasNext()) {
            final SAMRecord rec = iterator.next();
            final SAMRecord rec2 = rec.getReadPairedFlag() && iterator.hasNext() ? iterator.next() : null;
            rec.setAttribute(ReservedTagConstants.XT, null);

            // Do the clipping one way for PE and another for SE reads
            if (rec.getReadPairedFlag()) {
                // Assert that the input file is in query name order only if we see some PE reads
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        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" );
            out.close();
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            validator.setIgnoreWarnings(true);
            validator.setVerbose(true, 1000);
            validator.setErrorsToIgnore(Arrays.asList(SAMValidationError.Type.MISSING_READ_GROUP));
            SAMFileReader samReader = new SAMFileReader(getOutput());
            samReader.setValidationStringency(ValidationStringency.LENIENT);
            final SAMRecordIterator iterator = samReader.iterator();
            while (iterator.hasNext()) {
                final SAMRecord rec = iterator.next();
                Assert.assertEquals(rec.getCigarString(), expectedCigar);
                if (SAMUtils.hasMateCigar(rec)) {
                    Assert.assertEquals(SAMUtils.getMateCigarString(rec), expectedCigar);
                }
            }
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                Arrays.asList(SamPairUtil.PairOrientation.FR), SAMFileHeader.SortOrder.coordinate,
                new BestMapqPrimaryAlignmentSelectionStrategy(), false);

        merger.mergeAlignment();
        Assert.assertEquals(sorted, !merger.getForceSort());
        final SAMRecordIterator it = new SAMFileReader(target).iterator();
        int aln = 0;
        while (it.hasNext()) {
            final SAMRecord rec = it.next();
            if (!rec.getReadUnmappedFlag()) {
                aln++;
            }
        }
        Assert.assertEquals(aln, 6, "Incorrect number of aligned reads in merged BAM file");
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                                                final Integer expectedPrimaryHitIndex, final int expectedNumFirst,
                                                final int expectedNumSecond, final int expectedPrimaryMapq) throws Exception {

        // Create the aligned file by copying bases, quals, readname from the unmapped read, and conforming to each HitSpec.
        final File unmappedSam = new File(TEST_DATA_DIR, "multihit.filter.unmapped.sam");
        final SAMRecordIterator unmappedSamFileIterator = new SAMFileReader(unmappedSam).iterator();
        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());
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                                                final Integer expectedPrimaryHitIndex, final int expectedNumReads,
                                                final int expectedPrimaryMapq) throws Exception {

        // Create the aligned file by copying bases, quals, readname from the unmapped read, and conforming to each HitSpec.
        final File unmappedSam = new File(TEST_DATA_DIR, "multihit.filter.fragment.unmapped.sam");
        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());
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Related Classes of htsjdk.samtools.SAMRecordIterator

  • org.broad.igv.sam.reader.BAMFileReader
  • org.broad.igv.sam.SAMWriterTest
  • org.broadinstitute.gatk.engine.walkers.diffengine.BAMDiffableReader
  • org.broadinstitute.gatk.utils.locusiterator.LIBSPerformance
  • picard.illumina.MarkIlluminaAdapters
  • picard.sam.MergeBamAlignmentTest
  • picard.sam.ReorderSam
  • picard.sam.testers.CleanSamTester
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