Package org.broad.igv.sam.reader

Examples of org.broad.igv.sam.reader.SAMReader

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public class AlignmentIOTest extends AbstractHeadlessTest {

    @Test
    public void testEncodeDecode() throws Exception {
        String testFile = TestUtils.DATA_DIR + "sam/NA12878.muc1.test.sam";
        SAMReader reader = new SAMReader(testFile);

        Iterator<PicardAlignment> inputAlignmentIterator = reader.iterator();
        ArrayList<PicardAlignment> inputAlignmentList = new ArrayList<PicardAlignment>();

        while (inputAlignmentIterator.hasNext()) {
            PicardAlignment al = inputAlignmentIterator.next();
            inputAlignmentList.add(al);
        }
        ByteArrayOutputStream bos = new ByteArrayOutputStream();
        FeatureEncoder<PicardAlignment> alignmentEncoder = new SamAlignmentEncoder();
        alignmentEncoder.encodeAll(bos, reader.iterator());

        ByteArrayInputStream bis = new ByteArrayInputStream(bos.toByteArray());

        FeatureDecoder<PicardAlignment> alignmentDecoder = new AlignmentDecoder();
        Iterator<PicardAlignment> decodedAlignments = alignmentDecoder.decodeAll(bis, false);
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        int start = 153426040;
        int end = 153426154;

        // Test posA query that includes overlaps (contained == false)
        boolean contained = false;
        SAMReader reader = new SAMReader(testFile);
        CloseableIterator<PicardAlignment> iter = reader.query(chr, start, end, contained);
        int count = 0;
        while (iter.hasNext()) {
            Alignment record = iter.next();
            if (record.isMapped()) {
                assertEquals(chr, record.getChr());
                assertTrue(record.getEnd() >= start);
                assertTrue(record.getStart() <= end);
            }
            count++;
        }
        assertEquals(64, count);
        iter.close();
        reader.close();
    }
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        int start = 125963167;
        int end = 125972750;

        // Test posA query that includes overlaps (contained == false)
        boolean contained = false;
        SAMReader reader = new SAMReader(testFile);
        CloseableIterator<PicardAlignment> iter = reader.query(chr, start, end, contained);
        int count = 0;
        while (iter.hasNext()) {
            Alignment record = iter.next();
            assertEquals(chr, record.getChr());
            assertTrue(record.getEnd() >= start);
            assertTrue(record.getStart() <= end);
            count++;
        }
        assertEquals(329, count);
        iter.close();
        reader.close();

    }
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        int start = 12550532;
        int end = 12550610;

        // Test posA query that includes overlaps (contained == false)
        boolean contained = false;
        SAMReader reader = new SAMReader(testFile);
        CloseableIterator<PicardAlignment> iter = reader.query(chr, start, end, contained);
        int count = 0;
        while (iter.hasNext()) {
            Alignment record = iter.next();
            assertEquals(chr, record.getChr());
            assertTrue(record.getEnd() >= start);
            assertTrue(record.getStart() <= end);
            count++;
        }
        assertEquals(2, count);
        iter.close();
        reader.close();

    }
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        int end = 800152;

        // Test posA query that includes overlaps (contained == false)
        boolean contained = false;

        SAMReader reader = new SAMReader(testFile);
        CloseableIterator<PicardAlignment> iter = reader.query(chr, start, end, contained);
        int count = 0;
        while (iter.hasNext()) {
            Alignment record = iter.next();
            assertEquals(chr, record.getChr());
            assertTrue(record.getEnd() >= start);
            assertTrue(record.getStart() <= end);
            count++;
        }
        assertEquals(134, count);
        iter.close();
        reader.close();
    }
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        String chr = "chr1";
        int end = 300000000;
        int start = end / 5;

        BAMFileReader bamreader = new BAMFileReader(new File(bamfile));
        SAMReader samreader = new SAMReader(samfile);
        CloseableIterator<PicardAlignment> bamiter = bamreader.query(chr, start, end, true);
        CloseableIterator<PicardAlignment> samiter = samreader.iterator();
        int count = 0;
        while (bamiter.hasNext()) {
            Alignment bamrecord = bamiter.next();
            Alignment samrecord = samiter.next();
            assertTrue(bamrecord.getStart() >= start);
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        private SAMFileHeader header;
        private List<PicardAlignment> alignments;

        public SamHeaderIterator(String inpath) throws IOException {

            SAMReader reader = new SAMReader(inpath, false);
            this.header = reader.getFileHeader();
            Iterator<PicardAlignment> iter = reader.iterator();

            alignments = new ArrayList<PicardAlignment>();
            while (iter.hasNext()) {
                alignments.add(iter.next());
            }
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Related Classes of org.broad.igv.sam.reader.SAMReader

  • htsjdk.samtools.SAMFileReader
  • htsjdk.samtools.seekablestream.SeekableStream
  • org.broad.igv.cli_plugin.AlignmentIOTest
  • org.broad.igv.sam.BAMFileReaderTest
  • org.broad.igv.sam.SamQueryTextReaderTest
  • org.broad.igv.sam.SAMWriterTest$SamHeaderIterator
  • org.broad.igv.util.ResourceLocator
  • java.io.InputStream
  • java.io.BufferedInputStream
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