org.broadinstitute.hellbender.tools.ConvertHeaderlessHadoopBamShardToBam Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of gatk Show documentation
Development on GATK 4
The newest version!
package org.broadinstitute.hellbender.tools;

import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import htsjdk.samtools.ValidationStringency;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.BetaFeature;
import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
import org.broadinstitute.barclay.help.DocumentedFeature;
import org.broadinstitute.hellbender.cmdline.CommandLineProgram;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
import org.broadinstitute.hellbender.exceptions.UserException;
import org.broadinstitute.hellbender.utils.spark.SparkUtils;
import picard.cmdline.programgroups.ReadDataManipulationProgramGroup;

import java.io.File;
import java.io.IOException;


/**
 * This is a troubleshooting utility that converts a headerless BAM shard (e.g., a part-r-00000.bam, part-r-00001.bam, etc.),
 * produced by a Spark tool with --sharded-output set to true, into a readable BAM file by adding a header and a BGZF terminator.
 *
 * This tool is not intended for use with BAM shards that already have a header -- these shards are
 * already readable using samtools.
 *
 * Input
 * 
 *     A headerless BAM shard
 *     A well-formed BAM whose header will be used for the converted fragment
 * 
 *
 * Output
 * 
 *     The converted BAM shard
 * 
 *
 * Usage example
 *  * gatk ConvertHeaderlessHadoopBamShardToBam \
 *     --bam-shard part-r-00000.bam \
 *     --bam-with-header input.bam \
 *     -O output.bam
 * 
 */
@DocumentedFeature
@CommandLineProgramProperties(
        summary = "This is a troubleshooting utility that converts a headerless BAM shard (e.g., a part-r-00000.bam, part-r-00001.bam, etc.)," +
                " produced by a Spark tool with --sharded-output set to true, into a readable BAM file by adding a header and a BGZF terminator.",
        oneLineSummary = "Convert a headerless BAM shard into a readable BAM",
        programGroup = ReadDataManipulationProgramGroup.class
)
@BetaFeature
public final class ConvertHeaderlessHadoopBamShardToBam extends CommandLineProgram {

    public static final String BAM_SHARD_LONG_NAME = "bam-shard";
    public static final String BAM_WITH_HEADER_LONG_NAME = "bam-with-header";
    public static final String OUTPUT_LONG_NAME = StandardArgumentDefinitions.OUTPUT_LONG_NAME;
    public static final String OUTPUT_SHORT_NAME = StandardArgumentDefinitions.OUTPUT_SHORT_NAME;

    @Argument(fullName = BAM_SHARD_LONG_NAME, doc = "Headerless Hadoop BAM shard to be converted into a readable BAM", optional = false)
    private File bamShard = null;

    @Argument(fullName = BAM_WITH_HEADER_LONG_NAME, doc = "Well-formed BAM whose header to use for the converted fragment", optional = false)
    private File bamWithHeader = null;

    @Argument(shortName = OUTPUT_SHORT_NAME, fullName = OUTPUT_LONG_NAME, doc = "Location to write the converted BAM shard", optional = false)
    private File outputBam = null;

    @Override
    protected Object doWork(){
        SAMFileHeader header = null;
        try ( final SamReader headerReader = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).open(bamWithHeader) ) {
            header = headerReader.getFileHeader();
        }
        catch ( IOException e ) {
            throw new UserException("Error reading header from " + bamWithHeader.getAbsolutePath(), e);
        }

        SparkUtils.convertHeaderlessHadoopBamShardToBam(bamShard, header, outputBam);
        return null;
    }
}