// Path: src/main/java/org/seqdoop/hadoop_bam/util/SAMHeaderReader.java
// public final class SAMHeaderReader {
// 	/** A String property corresponding to a ValidationStringency
// 	 * value. If set, the given stringency is used when any part of the
// 	 * Hadoop-BAM library reads SAM or BAM.
// 	 */
// 	public static final String VALIDATION_STRINGENCY_PROPERTY =
// 		"hadoopbam.samheaderreader.validation-stringency";
// 
// 	public static SAMFileHeader readSAMHeaderFrom(Path path, Configuration conf)
// 		throws IOException
// 	{
// 		InputStream i = path.getFileSystem(conf).open(path);
// 		final SAMFileHeader h = readSAMHeaderFrom(i, conf);
// 		i.close();
// 		return h;
// 	}
// 
// 	/** Does not close the stream. */
// 	public static SAMFileHeader readSAMHeaderFrom(
// 		final InputStream in, final Configuration conf)
// 	{
// 		final ValidationStringency
// 			stringency = getValidationStringency(conf);
// 		SamReaderFactory readerFactory = SamReaderFactory.makeDefault()
// 				.setOption(SamReaderFactory.Option.EAGERLY_DECODE, false)
// 				.setUseAsyncIo(false);
// 		if (stringency != null) {
// 			readerFactory.validationStringency(stringency);
// 		}
// 
// 		final ReferenceSource refSource = getReferenceSource(conf);
// 		if (null != refSource) {
// 			readerFactory.referenceSource(refSource);
// 		}
// 		return readerFactory.open(SamInputResource.of(in)).getFileHeader();
// 	}
// 
// 	public static ValidationStringency getValidationStringency(
// 		final Configuration conf)
// 	{
// 		final String p = conf.get(VALIDATION_STRINGENCY_PROPERTY);
// 		return p == null ? null : ValidationStringency.valueOf(p);
// 	}
// 
// 	public static ReferenceSource getReferenceSource(
// 			final Configuration conf)
// 	{
// 		//TODO: There isn't anything particularly CRAM-specific about reference source or validation
// 		// stringency other than that a reference source is required for CRAM files. We should move
// 		// the reference source and validation stringency property names and utility methods out of
// 		// CRAMInputFormat and SAMHeaderReader and combine them together into a single class for extracting
// 		// configuration params, but it would break backward compatibility with existing code that
// 		// is dependent on the CRAMInputFormat.REFERENCE_SOURCE_PATH_PROPERTY.
// 		final String refSourcePath = conf.get(CRAMInputFormat.REFERENCE_SOURCE_PATH_PROPERTY);
// 		return refSourcePath == null ? null : new ReferenceSource(NIOFileUtil.asPath(refSourcePath));
// 	}
// }


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;
package org.seqdoop.hadoop_bam;





/** Writes only the BAM records, not the key.
 *
 * <p>A {@link SAMFileHeader} must be provided via {@link #setSAMHeader} or
 * {@link #readSAMHeaderFrom} before {@link #getRecordWriter} is called.</p>
 *
 * <p>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.</p>
 */
public class KeyIgnoringCRAMOutputFormat<K> extends CRAMOutputFormat<K> {
    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
    {
// Path: src/main/java/org/seqdoop/hadoop_bam/util/SAMHeaderReader.java
// public final class SAMHeaderReader {
// 	/** A String property corresponding to a ValidationStringency
// 	 * value. If set, the given stringency is used when any part of the
// 	 * Hadoop-BAM library reads SAM or BAM.
// 	 */
// 	public static final String VALIDATION_STRINGENCY_PROPERTY =
// 		"hadoopbam.samheaderreader.validation-stringency";
// 
// 	public static SAMFileHeader readSAMHeaderFrom(Path path, Configuration conf)
// 		throws IOException
// 	{
// 		InputStream i = path.getFileSystem(conf).open(path);
// 		final SAMFileHeader h = readSAMHeaderFrom(i, conf);
// 		i.close();
// 		return h;
// 	}
// 
// 	/** Does not close the stream. */
// 	public static SAMFileHeader readSAMHeaderFrom(
// 		final InputStream in, final Configuration conf)
// 	{
// 		final ValidationStringency
// 			stringency = getValidationStringency(conf);
// 		SamReaderFactory readerFactory = SamReaderFactory.makeDefault()
// 				.setOption(SamReaderFactory.Option.EAGERLY_DECODE, false)
// 				.setUseAsyncIo(false);
// 		if (stringency != null) {
// 			readerFactory.validationStringency(stringency);
// 		}
// 
// 		final ReferenceSource refSource = getReferenceSource(conf);
// 		if (null != refSource) {
// 			readerFactory.referenceSource(refSource);
// 		}
// 		return readerFactory.open(SamInputResource.of(in)).getFileHeader();
// 	}
// 
// 	public static ValidationStringency getValidationStringency(
// 		final Configuration conf)
// 	{
// 		final String p = conf.get(VALIDATION_STRINGENCY_PROPERTY);
// 		return p == null ? null : ValidationStringency.valueOf(p);
// 	}
// 
// 	public static ReferenceSource getReferenceSource(
// 			final Configuration conf)
// 	{
// 		//TODO: There isn't anything particularly CRAM-specific about reference source or validation
// 		// stringency other than that a reference source is required for CRAM files. We should move
// 		// the reference source and validation stringency property names and utility methods out of
// 		// CRAMInputFormat and SAMHeaderReader and combine them together into a single class for extracting
// 		// configuration params, but it would break backward compatibility with existing code that
// 		// is dependent on the CRAMInputFormat.REFERENCE_SOURCE_PATH_PROPERTY.
// 		final String refSourcePath = conf.get(CRAMInputFormat.REFERENCE_SOURCE_PATH_PROPERTY);
// 		return refSourcePath == null ? null : new ReferenceSource(NIOFileUtil.asPath(refSourcePath));
// 	}
// }


// Path: src/main/java/org/seqdoop/hadoop_bam/KeyIgnoringCRAMOutputFormat.java
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;

package org.seqdoop.hadoop_bam;





/** Writes only the BAM records, not the key.
 *
 * <p>A {@link SAMFileHeader} must be provided via {@link #setSAMHeader} or
 * {@link #readSAMHeaderFrom} before {@link #getRecordWriter} is called.</p>
 *
 * <p>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.</p>
 */
public class KeyIgnoringCRAMOutputFormat<K> extends CRAMOutputFormat<K> {
    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);