Examples with VCFCodec htsjdk.variant.vcf.VCFCodec used on opensource projects

Example 21 with VCFCodec

use of htsjdk.variant.vcf.VCFCodec in project jvarkit by lindenb.

the class KnimeVariantHelper method indexVcfFile.

/**
 * index a vcf file is needed
 */
public void indexVcfFile(final File file) throws IOException {
    IOUtil.assertFileIsReadable(file);
    if (file.getName().endsWith(".vcf.gz")) {
        LOG.info("writing tabix index for " + file);
        final File output = new File(file.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION);
        try {
            if (output.exists()) {
                getLogger().info("Tabix index " + output + " already exists.");
                return;
            }
            final TabixIndex index = IndexFactory.createTabixIndex(file, new VCFCodec(), (SAMSequenceDictionary) null);
            index.write(output);
        } catch (final Exception err) {
            LOG.error(err);
            throw new IOException(err);
        }
    } else if (file.getName().endsWith(".vcf")) {
        LOG.info("writing tribble index for " + file);
        final File output = new File(file.getAbsolutePath() + Tribble.STANDARD_INDEX_EXTENSION);
        try {
            if (output.exists()) {
                getLogger().info("Tribble index " + output + " already exists.");
            }
            final Index index = IndexFactory.createIndex(file, new VCFCodec(), IndexType.LINEAR);
            index.writeBasedOnFeatureFile(file);
        } catch (final Exception err) {
            LOG.error(err);
            throw new IOException(err);
        }
    } else {
        throw new IOException("Cannot index VCF file " + file);
    }
}