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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

// Copyright (c) 2012 Aalto University
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to
// deal in the Software without restriction, including without limitation the
// rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
// sell copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
// IN THE SOFTWARE.

// File created: 2012-02-23 14:06:35

package org.seqdoop.hadoop_bam;

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

import org.apache.hadoop.fs.Path;

/** Describes a SAM format. */
public enum SAMFormat {
	SAM, BAM, CRAM;

	/** Infers the SAM format by looking at the filename of the given path.
	 *
	 * @see #inferFromFilePath(String)
	 */
	public static SAMFormat inferFromFilePath(final Path path) {
		return inferFromFilePath(path.getName());
	}

	/** Infers the SAM format by looking at the extension of the given file
	 * name. *.sam is recognized as {@link #SAM},
	 * *.bam as {@link #BAM}, and *.bam as {@link #CRAM}.
	 */
	public static SAMFormat inferFromFilePath(final String name) {
		if (name.endsWith(".bam")) return BAM;
		if (name.endsWith(".cram")) return CRAM;
		if (name.endsWith(".sam")) return SAM;
		return null;
	}

	public static SAMFormat inferFromData(final InputStream in) throws IOException {
		final byte b = (byte)in.read();
		in.close();
		switch (b) {
			case 0x1f: return SAMFormat.BAM;
			case 0x43: return SAMFormat.CRAM;
			case '@':  return SAMFormat.SAM;
		}
		return null;
	}
}