Package htsjdk.samtools

Examples of htsjdk.samtools.SAMRecord

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            @Override public boolean hasNext() { return ! engine.exceedsRuntimeLimit() && readIterator.hasNext(); }

            @Override
            public MapData next() {
                final SAMRecord read = readIterator.next();
                final ReferenceContext refContext = ! read.getReadUnmappedFlag()
                        ? reference.getReferenceContext(read)
                        : null;

                // if the read is mapped, create a metadata tracker
                final RefMetaDataTracker tracker = read.getReferenceIndex() >= 0
                        ? rodView.getReferenceOrderedDataForRead(read)
                        : null;

                // update the number of reads we've seen
                dataProvider.getShard().getReadMetrics().incrementNumIterations();
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        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";
            }

            DiffNode readRoot = DiffNode.empty(name, root);

            // add fields
            readRoot.add("NAME", record.getReadName());
            readRoot.add("FLAGS", record.getFlags());
            readRoot.add("RNAME", record.getReferenceName());
            readRoot.add("POS", record.getAlignmentStart());
            readRoot.add("MAPQ", record.getMappingQuality());
            readRoot.add("CIGAR", record.getCigarString());
            readRoot.add("RNEXT", record.getMateReferenceName());
            readRoot.add("PNEXT", record.getMateAlignmentStart());
            readRoot.add("TLEN", record.getInferredInsertSize());
            readRoot.add("SEQ", record.getReadString());
            readRoot.add("QUAL", record.getBaseQualityString());

            for ( SAMRecord.SAMTagAndValue xt : record.getAttributes() ) {
                readRoot.add(xt.tag, xt.value);
            }

            // add record to root
            if ( ! root.hasElement(name) )
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            dataProvider= "UnsupportedCigarOperatorDataProvider")
    @CigarOperatorTest(CigarOperatorTest.Outcome.IGNORE)
    public void testCigarNOperatorFilterIgnore(final String cigarString) {

        final MalformedReadFilter filter = buildMalformedReadFilter(false);
        final SAMRecord nContainingCigarRead = buildSAMRecord(cigarString);
        Assert.assertFalse(filter.filterOut(nContainingCigarRead),
                "filters out N containing Cigar when it should ignore the fact");
    }
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    @Test(enabled = true, dataProvider= "UnsupportedCigarOperatorDataProvider")
    @CigarOperatorTest(CigarOperatorTest.Outcome.FILTER)
    public void testCigarNOperatorFilterTruePositive(String cigarString) {

       final MalformedReadFilter filter = buildMalformedReadFilter(true);
       final SAMRecord nContainingCigarRead = buildSAMRecord(cigarString);
       Assert.assertTrue(filter.filterOut(nContainingCigarRead),
                  " Did not filtered out a N containing CIGAR read");
    }
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        }

        Iterator<SAMRecord> iter = downsampledReads.iterator();
        Assert.assertTrue(iter.hasNext());

        SAMRecord previousRead = iter.next();
        int currentStackSize = 1;

        while ( iter.hasNext() ) {
            SAMRecord currentRead = iter.next();

            if ( currentRead.getReferenceIndex() > previousRead.getReferenceIndex() || currentRead.getAlignmentStart() > previousRead.getAlignmentStart() ) {
                stackSizes.add(currentStackSize);
                currentStackSize = 1;
            }
            else if ( currentRead.getReferenceIndex() < previousRead.getReferenceIndex() || currentRead.getAlignmentStart() < previousRead.getAlignmentStart() ) {
                Assert.fail(String.format("Reads are out of order: %s %s", previousRead, currentRead));
            }
            else {
                currentStackSize++;
            }
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        Assert.assertFalse(downsampler.hasFinalizedItems());
        Assert.assertTrue(downsampler.peekFinalized() == null);
        Assert.assertTrue(downsampler.hasPendingItems());
        Assert.assertTrue(downsampler.peekPending() != null);

        SAMRecord laterRead = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, 2, 100);
        downsampler.signalNoMoreReadsBefore(laterRead);

        Assert.assertTrue(downsampler.hasFinalizedItems());
        Assert.assertTrue(downsampler.peekFinalized() != null);
        Assert.assertFalse(downsampler.hasPendingItems());
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            if ( verifySortedness ) {
                downsamplingIter = new VerifyingSamIterator(downsamplingIter);
            }

            while ( downsamplingIter.hasNext() ) {
                SAMRecord read = downsamplingIter.next();
                String sampleName = read.getReadGroup() != null ? read.getReadGroup().getSample() : null;

                ArtificialSingleSampleReadStreamAnalyzer analyzer = perSampleStreamAnalyzers.get(sampleName);
                if ( analyzer != null ) {
                    analyzer.update(read);
                }
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    @Test(enabled = true, dataProvider= "UnsupportedCigarOperatorDataProvider")
    @CigarOperatorTest(CigarOperatorTest.Outcome.ACCEPT)
    public void testCigarNOperatorFilterTrueNegative(String cigarString) {

        final MalformedReadFilter filter = buildMalformedReadFilter(true);
        final SAMRecord nonNContainingCigarRead = buildSAMRecord(cigarString);
        Assert.assertFalse(filter.filterOut(nonNContainingCigarRead),
                    " Filtered out a non-N containing CIGAR read");
    }
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            dataProvider= "UnsupportedCigarOperatorDataProvider")
    @CigarOperatorTest(CigarOperatorTest.Outcome.EXCEPTION)
    public void testCigarNOperatorFilterException(final String cigarString) {

        final MalformedReadFilter filter = buildMalformedReadFilter(false);
        final SAMRecord nContainingCigarRead = buildSAMRecord(cigarString);

        filter.filterOut(nContainingCigarRead);
    }
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    @Test(enabled = true, dataProvider="UnsupportedCigarOperatorDataProvider")
    @CigarOperatorTest(CigarOperatorTest.Outcome.ACCEPT)
    public void testCigarNOperatorFilterControl(final String cigarString) {

        final MalformedReadFilter filter = buildMalformedReadFilter(false);
        final SAMRecord nonNContainingCigarRead = buildSAMRecord(cigarString);

        Assert.assertFalse(filter.filterOut(nonNContainingCigarRead));
    }
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Related Classes of htsjdk.samtools.SAMRecord

  • org.broad.igv.sam.PicardAlignment
  • org.broad.igv.sam.reader.SAMFileGroup$SamGroupIterator
  • org.broad.igv.sam.reader.SAMQueryIterator
  • org.broadinstitute.gatk.engine.datasources.reads.IntervalOverlapFilteringIterator
  • org.broadinstitute.gatk.engine.datasources.reads.IntervalOverlapFilteringIteratorUnitTest
  • org.broadinstitute.gatk.engine.datasources.reads.PicardBaselineBenchmark
  • org.broadinstitute.gatk.engine.datasources.reads.TheoreticalMinimaBenchmark
  • org.broadinstitute.gatk.engine.downsampling.DownsamplingReadsIterator
  • org.broadinstitute.gatk.engine.downsampling.PerSampleDownsamplingReadsIterator
  • org.broadinstitute.gatk.engine.downsampling.PerSampleDownsamplingReadsIteratorUnitTest$PerSampleDownsamplingReadsIteratorTest
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