Package htsjdk.samtools

Examples of htsjdk.samtools.SAMRecord

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     */
    public SAMRecord next() {
        if (next == null) {
            throw new NoSuchElementException("Iterator has no more elements.");
        }
        final SAMRecord result = next;
        next = getNextRecord();
        return result;
    }
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     *
     * @return SAMRecord    the next filter-passing record
     */
    private SAMRecord getNextRecord() {
        while (iterator.hasNext()) {
            SAMRecord record = iterator.next();

            // update only the private copy of the metrics so that we don't need to worry about race conditions
            // that can arise when trying to update the global copy; it was agreed that this is the cleanest solution.
            privateRuntimeMetrics.incrementNumReadsSeen();

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    }

    @Test
    public void testBasicCount() {
        for (int x = 1; x <= 100; x++) {
            SAMRecord rec = ArtificialSAMUtils.createArtificialRead(header, String.valueOf(x), 1, x, ArtificialSAMUtils.DEFAULT_READ_LENGTH);
            writer.addAlignment(rec);
        }
        assertEquals(writer.getRecords().size(), 100);

    }
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    public void testReadName() {
        List<String> names = new ArrayList<String>();

        for (int x = 1; x <= 100; x++) {
            names.add(String.valueOf(x));
            SAMRecord rec = ArtificialSAMUtils.createArtificialRead(header, String.valueOf(x), 1, x, ArtificialSAMUtils.DEFAULT_READ_LENGTH);
            writer.addAlignment(rec);
        }
        assertEquals(writer.getRecords().size(), 100);

        // check the names
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        Assert.assertTrue(reader.hasIndex());
        final Iterator<SAMRecord> bamIt = reader.iterator();
        int nReadsFromBam = 0;
        int lastStart = -1;
        while ( bamIt.hasNext() ) {
            final SAMRecord read = bamIt.next();
            assertGoodRead(read, bamBuilder);
            nReadsFromBam++;
            Assert.assertTrue(read.getAlignmentStart() >= lastStart);
            lastStart = read.getAlignmentStart();
        }
        Assert.assertEquals(nReadsFromBam, bamBuilder.expectedNumberOfReads());
    }
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    public void testWholeChromosomeQuery() {
        ArtificialSAMQueryIterator iter = ArtificialSAMUtils.queryReadIterator(1, 2, 100);
        iter.queryContained("chr1", 1, -1);
        int count = 0;
        while (iter.hasNext()) {
            SAMRecord rec = iter.next();
            count++;
        }
        assertEquals(count, 100);

    }
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    public void testContainedQueryStart() {
        ArtificialSAMQueryIterator iter = ArtificialSAMUtils.queryReadIterator(1, 2, 100);
        iter.queryContained("chr1", 1, 50);
        int count = 0;
        while (iter.hasNext()) {
            SAMRecord rec = iter.next();
            count++;
        }
        assertEquals(count, 1);

    }
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    public void testOverlappingQueryStart() {
        ArtificialSAMQueryIterator iter = ArtificialSAMUtils.queryReadIterator(1, 2, 100);
        iter.queryOverlapping("chr1", 1, 50);
        int count = 0;
        while (iter.hasNext()) {
            SAMRecord rec = iter.next();
            count++;
        }
        assertEquals(count, 50);

    }
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    public void testContainedQueryMiddle() {
        ArtificialSAMQueryIterator iter = ArtificialSAMUtils.queryReadIterator(1, 2, 100);
        iter.queryContained("chr1", 25, 74);
        int count = 0;
        while (iter.hasNext()) {
            SAMRecord rec = iter.next();
            count++;
        }
        assertEquals(count, 1);

    }
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    public void testOverlappingQueryMiddle() {
        ArtificialSAMQueryIterator iter = ArtificialSAMUtils.queryReadIterator(1, 2, 100);
        iter.queryOverlapping("chr1", 25, 74);
        int count = 0;
        while (iter.hasNext()) {
            SAMRecord rec = iter.next();
            count++;
        }
        assertEquals(count, 50);

    }
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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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