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A Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework.

There is a newer version: 7.10.0

package org.seqdoop.hadoop_bam;

import java.io.IOException;
import java.io.InputStream;

import htsjdk.samtools.SAMFileHeader;

import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.mapreduce.RecordWriter;
import org.apache.hadoop.mapreduce.TaskAttemptContext;

import org.seqdoop.hadoop_bam.util.SAMHeaderReader;

/** Writes only the BAM records, not the key.
 *
 * A {@link SAMFileHeader} must be provided via {@link #setSAMHeader} or
 * {@link #readSAMHeaderFrom} before {@link #getRecordWriter} is called.
 *
 * By default, writes the SAM header to the output file(s). This
 * can be disabled, because in distributed usage one often ends up with (and,
 * for decent performance, wants to end up with) the output split into multiple
 * parts, which are easier to concatenate if the header is not present in each
 * file.
 */
public class KeyIgnoringCRAMOutputFormat extends CRAMOutputFormat {
    protected SAMFileHeader header;
    private boolean writeHeader = true;

    public KeyIgnoringCRAMOutputFormat() {}

    /** Whether the header will be written or not. */
    public boolean getWriteHeader()          { return writeHeader; }

    /** Set whether the header will be written or not. */
    public void    setWriteHeader(boolean b) { writeHeader = b; }

    public SAMFileHeader getSAMHeader() { return header; }
    public void setSAMHeader(SAMFileHeader header) { this.header = header; }

    public void readSAMHeaderFrom(Path path, Configuration conf)
            throws IOException
    {
        this.header = SAMHeaderReader.readSAMHeaderFrom(path, conf);
    }
    public void readSAMHeaderFrom(InputStream in, Configuration conf) {
        this.header = SAMHeaderReader.readSAMHeaderFrom(in, conf);
    }

    /** setSAMHeader or readSAMHeaderFrom must have
     * been called first.
     */
    @Override public RecordWriter getRecordWriter(
            TaskAttemptContext ctx)
            throws IOException
    {
        return getRecordWriter(ctx, getDefaultWorkFile(ctx, ""));
    }

    // Allows wrappers to provide their own work file.
    public RecordWriter getRecordWriter(
            TaskAttemptContext ctx, Path out)
            throws IOException
    {
        if (this.header == null)
            throw new IOException(
                    "Can't create a RecordWriter without the SAM header");

        return new KeyIgnoringCRAMRecordWriter(out, header, writeHeader, ctx);
    }
}