htsjdk.beta.codecs.reads.bam.bamV1_0.BAMDecoderV1_0 Maven / Gradle / Ivy

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A Java API for high-throughput sequencing data (HTS) formats
There is a newer version: 4.1.3
package htsjdk.beta.codecs.reads.bam.bamV1_0;

import htsjdk.beta.codecs.reads.ReadsCodecUtils;
import htsjdk.beta.codecs.reads.bam.BAMDecoder;
import htsjdk.beta.io.bundle.Bundle;
import htsjdk.beta.io.bundle.BundleResourceType;
import htsjdk.beta.plugin.interval.HtsIntervalUtils;
import htsjdk.beta.exception.HtsjdkIOException;
import htsjdk.beta.plugin.HtsVersion;
import htsjdk.beta.plugin.interval.HtsInterval;
import htsjdk.beta.plugin.interval.HtsQueryRule;

import htsjdk.beta.plugin.reads.ReadsDecoderOptions;
import htsjdk.samtools.QueryInterval;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import htsjdk.samtools.util.CloseableIterator;
import htsjdk.utils.ValidationUtils;

import java.io.IOException;
import java.util.List;
import java.util.Optional;

/**
  * BAM v1.0 decoder.
 */
public class BAMDecoderV1_0 extends BAMDecoder {
    private final SamReader samReader;
    private final SAMFileHeader samFileHeader;

    /**
     * Create a V1.0 BAM decoder for the given input bundle. The primary resource in the bundle must
     * have content type {@link BundleResourceType#ALIGNED_READS}, and the resource must be an
     * appropriate format and version for this encoder (to find an encoder for a bundle, see
     * {@link htsjdk.beta.plugin.registry.ReadsResolver}.
     *
     * @param inputBundle bundle to decoder
     * @param readsDecoderOptions options to use
     */
    public BAMDecoderV1_0(final Bundle inputBundle, final ReadsDecoderOptions readsDecoderOptions) {
        super(inputBundle, readsDecoderOptions);
        samReader = ReadsCodecUtils.getSamReader(inputBundle, readsDecoderOptions, SamReaderFactory.makeDefault());
        samFileHeader = samReader.getFileHeader();
    }

    @Override
    public HtsVersion getVersion() {
        return BAMCodecV1_0.VERSION_1;
    }

    @Override
    public SAMFileHeader getHeader() {
        return samFileHeader;
    }

    // HtsQuery methods

    @Override
    public CloseableIterator iterator() {
        return samReader.iterator();
    }

    @Override
    public boolean isQueryable() {
        return ReadsCodecUtils.bundleContainsIndex(getInputBundle()) && samReader.isQueryable();
    }

    @Override
    public boolean hasIndex() {
        return ReadsCodecUtils.bundleContainsIndex(getInputBundle()) && samReader.hasIndex();
    }

    @Override
    public CloseableIterator query(final List intervals, final HtsQueryRule queryRule) {
        ValidationUtils.nonNull(intervals, "intervals");
        ValidationUtils.nonNull(queryRule, "queryRule");

        ReadsCodecUtils.assertBundleContainsIndex(getInputBundle());
        final QueryInterval[] queryIntervals = HtsIntervalUtils.toQueryIntervalArray(
                intervals,
                samFileHeader.getSequenceDictionary());
        return samReader.query(queryIntervals, queryRule == HtsQueryRule.CONTAINED);
    }

    @Override
    public CloseableIterator queryStart(final String queryName, final long start) {
        ValidationUtils.nonNull(queryName, "queryName");

        ReadsCodecUtils.assertBundleContainsIndex(getInputBundle());
        return samReader.queryAlignmentStart(queryName, HtsIntervalUtils.toIntegerSafe(start));
    }

    // ReadsQuery interface methods

    @Override
    public CloseableIterator queryUnmapped() {
        ReadsCodecUtils.assertBundleContainsIndex(getInputBundle());
        return samReader.queryUnmapped();
    }

    @Override
    public Optional queryMate(final SAMRecord samRecord) {
        ValidationUtils.nonNull(samRecord, "samRecord");

        ReadsCodecUtils.assertBundleContainsIndex(getInputBundle());
        return Optional.ofNullable(samReader.queryMate(samRecord));
    }

    @Override
    public void close() {
        try {
            samReader.close();
        } catch (IOException e) {
            throw new HtsjdkIOException(String.format("Exception closing reader for %s", getInputBundle()), e);
        }
    }

}