htsjdk.samtools.SAMSequenceDictionary#addSequence

Source File: BGZF_ReferenceSequenceFile.java From cramtools with Apache License 2.0

6 votes

public BGZF_ReferenceSequenceFile(File file) throws FileNotFoundException {
	if (!file.canRead())
		throw new RuntimeException("Cannot find or read fasta file: " + file.getAbsolutePath());

	File indexFile = new File(file.getAbsolutePath() + ".fai");
	if (!indexFile.canRead())
		throw new RuntimeException("Cannot find or read fasta index file: " + indexFile.getAbsolutePath());

	Scanner scanner = new Scanner(indexFile);
	int seqID = 0;
	dictionary = new SAMSequenceDictionary();
	while (scanner.hasNextLine()) {
		String line = scanner.nextLine();
		FAIDX_FastaIndexEntry entry = FAIDX_FastaIndexEntry.fromString(seqID++, line);
		index.put(entry.getName(), entry);
		dictionary.addSequence(new SAMSequenceRecord(entry.getName(), entry.getLen()));
	}
	scanner.close();

	if (index.isEmpty())
		log.warn("No entries in the index: " + indexFile.getAbsolutePath());

	is = new BlockCompressedInputStream(new SeekableFileStream(file));
}

Source File: SamRegionRestrictionTest.java From rtg-tools with BSD 2-Clause "Simplified" License

6 votes

public void testSomeMethod() {
  SamRegionRestriction srr = new SamRegionRestriction("fooo");
  final SAMSequenceDictionary sdd = new SAMSequenceDictionary();
  sdd.addSequence(new SAMSequenceRecord("fooo", 9876));
  assertEquals(0, srr.resolveStart());
  assertEquals(9876, srr.resolveEnd(sdd));
  assertEquals("fooo", srr.getSequenceName());
  assertEquals(RegionRestriction.MISSING, srr.getStart());
  assertEquals(RegionRestriction.MISSING, srr.getEnd());
  assertEquals("fooo", srr.toString());

  srr = new SamRegionRestriction("fooo", 75, 555);
  assertEquals(75, srr.resolveStart());
  assertEquals(555, srr.resolveEnd(sdd));
  assertEquals("fooo", srr.getSequenceName());
  assertEquals(75, srr.getStart());
  assertEquals(555, srr.getEnd());
  assertEquals("fooo:76-555", srr.toString());
  srr = new SamRegionRestriction("fooo", 75, RegionRestriction.MISSING);
  assertEquals("fooo:76", srr.toString());
}

Source File: HaplotypeMapTest.java From picard with MIT License

6 votes

@DataProvider(name="haplotypeMapForWriting")
public Object[][] haplotypeMapForWriting() {

    SAMFileHeader header = new SAMFileHeader();
    header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
    SAMSequenceDictionary sd = new SAMSequenceDictionary();
    sd.addSequence(new SAMSequenceRecord("chr1", 101));
    sd.addSequence(new SAMSequenceRecord("chr2", 101));
    sd.addSequence(new SAMSequenceRecord("chr3", 101));
    header.setSequenceDictionary(sd);


    HaplotypeMap newMap = new HaplotypeMap(header);
    HaplotypeBlock t1 = new HaplotypeBlock(0.151560926);
    t1.addSnp(new Snp("snp2", "chr1", 83, (byte)'A', (byte)'G', .16, null));
    t1.addSnp(new Snp("snp1", "chr1", 51, (byte)'T', (byte)'C', 0.15, Collections.singletonList("SQNM_1CHIP_FingerprintAssays")));
    newMap.addHaplotype(t1);
    HaplotypeBlock t2 = new HaplotypeBlock(.02d);
    t2.addSnp(new Snp("snp3", "chr2", 24, (byte)'C', (byte)'A', .20, null));
    newMap.addHaplotype(t2);

    return new Object[][]{{newMap}};
}

Source File: PSFilterTest.java From gatk with BSD 3-Clause "New" or "Revised" License

6 votes

@Test(groups = "spark")
public void testDoSetPairFlags() {

    final JavaSparkContext ctx = SparkContextFactory.getTestSparkContext();
    final SAMSequenceDictionary seq = new SAMSequenceDictionary();
    seq.addSequence(new SAMSequenceRecord("test_seq", 1000));
    final SAMFileHeader header = new SAMFileHeader(seq);

    final List<GATKRead> readList = makeReadSet(header);
    final JavaRDD<GATKRead> reads = ctx.parallelize(readList);
    ;

    final List<GATKRead> result = PSFilter.setPairFlags(reads, 100).collect();

    Assert.assertEquals(result.size(), 6);
    for (final GATKRead read : result) {
        if (read.getName().equals("paired_1") || read.getName().equals("paired_2")) {
            Assert.assertTrue(read.isPaired());
        } else {
            Assert.assertFalse(read.isPaired());
        }
    }

}