Examples with SAMSequenceDictionaryCodec htsjdk.samtools.SAMSequenceDictionaryCodec used on opensource projects

Example 1 with SAMSequenceDictionaryCodec

use of htsjdk.samtools.SAMSequenceDictionaryCodec in project jvarkit by lindenb.

the class VcfSetSequenceDictionaryTest method test01.

@Test(dataProvider = "all-vcf-files")
public void test01(final String inputFile) throws IOException {
    final SAMSequenceDictionary dict = SAMSequenceDictionaryExtractor.extractDictionary(new File(inputFile));
    if (dict == null || dict.isEmpty())
        return;
    final File dictF = super.createTmpFile(".dict");
    final BufferedWriter bw = Files.newBufferedWriter(dictF.toPath());
    final SAMSequenceDictionaryCodec codec = new SAMSequenceDictionaryCodec(bw);
    codec.encode(new SAMSequenceDictionary(dict.getSequences().stream().map(S -> new SAMSequenceRecord(S.getSequenceName().startsWith("chr") ? S.getSequenceName().substring(3) : "chr" + S.getSequenceName(), S.getSequenceLength())).collect(Collectors.toList())));
    bw.flush();
    bw.close();
    final File output = super.createTmpFile(".vcf");
    Assert.assertEquals(0, new VcfSetSequenceDictionary().instanceMain(new String[] { "-o", output.getPath(), "-R", dictF.getPath(), inputFile }));
    assertIsVcf(output);
}