Examples with FeatureReader htsjdk.tribble.FeatureReader used on opensource projects

Example 1 with FeatureReader

use of htsjdk.tribble.FeatureReader in project gatk by broadinstitute.

the class GatherVcfs method getReaderFromVCFUri.

private static FeatureReader<VariantContext> getReaderFromVCFUri(final Path variantPath, final int cloudPrefetchBuffer) {
    final String variantURI = variantPath.toUri().toString();
    final Function<SeekableByteChannel, SeekableByteChannel> cloudWrapper = (cloudPrefetchBuffer > 0 ? is -> SeekableByteChannelPrefetcher.addPrefetcher(cloudPrefetchBuffer, is) : Function.identity());
    return AbstractFeatureReader.getFeatureReader(variantURI, null, new VCFCodec(), false, cloudWrapper, Function.identity());
}

Example 2 with FeatureReader

use of htsjdk.tribble.FeatureReader in project gatk by broadinstitute.

the class GenomicsDBImport method traverse.

/**
     * A complete traversal from start to finish. This method will import all samples
     * specified in the input GVCF files.
     */
@Override
public void traverse() {
    // Force the progress meter to update after every batch
    progressMeter.setRecordsBetweenTimeChecks(1L);
    final int sampleCount = sampleNameToVcfUri.size();
    final int updatedBatchSize = (batchSize == DEFAULT_ZERO_BATCH_SIZE) ? sampleCount : batchSize;
    final int totalBatchCount = (sampleCount / updatedBatchSize) + (sampleCount % updatedBatchSize == 0 ? 0 : 1);
    GenomicsDBImporter importer;
    for (int i = 0, batchCount = 1; i < sampleCount; i += updatedBatchSize, ++batchCount) {
        final Map<String, FeatureReader<VariantContext>> sampleToReaderMap = getFeatureReaders(new ArrayList<>(sampleNameToVcfUri.keySet()), sampleNameToVcfUri, updatedBatchSize, sampleCount, i);
        logger.info("Importing batch " + batchCount + " with " + sampleToReaderMap.size() + " samples");
        final long variantContextBufferSize = vcfBufferSizePerSample * sampleToReaderMap.size();
        final GenomicsDBImportConfiguration.ImportConfiguration importConfiguration = createImportConfiguration(workspace, GenomicsDBConstants.DEFAULT_ARRAY_NAME, variantContextBufferSize, segmentSize, i, (i + updatedBatchSize - 1));
        try {
            importer = new GenomicsDBImporter(sampleToReaderMap, mergedHeaderLines, intervals.get(0), importConfiguration);
        } catch (final IOException e) {
            throw new UserException("Error initializing GenomicsDBImporter in batch " + batchCount, e);
        }
        try {
            importer.importBatch();
        } catch (final IOException e) {
            throw new UserException("GenomicsDB import failed in batch " + batchCount, e);
        }
        closeReaders(sampleToReaderMap);
        progressMeter.update(intervals.get(0));
        logger.info("Done importing batch " + batchCount + "/" + totalBatchCount);
    }
}