/*
* The MIT License
*
* Copyright (c) 2009 The Broad Institute
*
* 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.
*/
package picard.sam;
import htsjdk.samtools.SAMFileHeader;import htsjdk.samtools.SAMFileReader;import htsjdk.samtools.SAMFileWriter;import htsjdk.samtools.SAMFileWriterFactory;import htsjdk.samtools.SAMReadGroupRecord;import htsjdk.samtools.SAMRecord;import picard.cmdline.CommandLineProgram;
import picard.cmdline.CommandLineProgramProperties;
import picard.cmdline.Option;
import picard.cmdline.StandardOptionDefinitions;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.Log;
import picard.cmdline.programgroups.SamOrBam;
import java.io.File;
import java.lang.Override;
import java.lang.String;
import java.lang.System;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
/**
* Command-line program to split a SAM or BAM file into separate files based on
* library name.
*
* @author ktibbett@broadinstitute.org
*/
@CommandLineProgramProperties(
usage = "Takes a SAM or BAM file and separates all the reads " +
"into one SAM or BAM file per library name. Reads that do not have " +
"a read group specified or whose read group does not have a library name " +
"are written to a file called 'unknown.' The format (SAM or BAM) of the " +
"output files matches that of the input file. ",
usageShort = "Splits a SAM or BAM file into individual files by library",
programGroup = SamOrBam.class
)
public class SplitSamByLibrary extends CommandLineProgram {
@Option(shortName= StandardOptionDefinitions.INPUT_SHORT_NAME,
doc="The SAM or BAM file to be split. ")
public File INPUT;
@Option(shortName=StandardOptionDefinitions.OUTPUT_SHORT_NAME,
doc="The directory where the library SAM or BAM files should be written " +
"(defaults to the current directory). ", optional=true )
public File OUTPUT = new File(".").getAbsoluteFile();
private static final Log log = Log.getInstance(SplitSamByLibrary.class);
public static final int NO_LIBRARIES_SPECIFIED_IN_HEADER = 2;
public static void main(String[] args) {
System.exit(new SplitSamByLibrary().instanceMain(args));
}
@Override
protected int doWork() {
IOUtil.assertFileIsReadable(INPUT);
IOUtil.assertDirectoryIsWritable(OUTPUT);
SAMFileReader reader = new SAMFileReader(INPUT);
Map<String, SAMFileWriter> libraryToWriter = new HashMap<String, SAMFileWriter>();
Map<String, List<SAMReadGroupRecord>> libraryToRg = new HashMap<String, List<SAMReadGroupRecord>>();
SAMFileWriterFactory factory = new SAMFileWriterFactory();
String extension = reader.isBinary() ? ".bam" : ".sam";
SAMFileHeader unknownHeader = reader.getFileHeader().clone();
unknownHeader.setReadGroups(new ArrayList<SAMReadGroupRecord>());
SAMFileWriter unknown = null;
for (SAMReadGroupRecord rg : reader.getFileHeader().getReadGroups()) {
String lib = rg.getLibrary();
if (lib != null) {
if (!libraryToRg.containsKey(lib)) {
libraryToRg.put(lib, new ArrayList<SAMReadGroupRecord>());
}
libraryToRg.get(lib).add(rg);
}
else {
unknownHeader.addReadGroup(rg);
}
}
if (libraryToRg.size() == 0) {
log.error("No individual libraries are " +
"specified in the header of " + INPUT.getAbsolutePath());
return NO_LIBRARIES_SPECIFIED_IN_HEADER;
}
for (Map.Entry<String, List<SAMReadGroupRecord>> entry : libraryToRg.entrySet()) {
String lib = entry.getKey();
SAMFileHeader header = reader.getFileHeader().clone();
header.setReadGroups(entry.getValue());
libraryToWriter.put(lib, factory.makeSAMOrBAMWriter(header, true,
new File(OUTPUT, IOUtil.makeFileNameSafe(lib) + extension)));
}
for (Iterator<SAMRecord> it = reader.iterator(); it.hasNext(); ) {
SAMRecord sam = it.next();
SAMReadGroupRecord rg = sam.getReadGroup();
if (rg != null && rg.getLibrary() != null) {
libraryToWriter.get(rg.getLibrary()).addAlignment(sam);
}
else {
if (unknown == null) {
unknown = factory.makeSAMOrBAMWriter(unknownHeader, true,
new File(OUTPUT, "unknown" + extension));
}
unknown.addAlignment(sam);
}
}
// Close the reader and writers
reader.close();
if (unknown != null) {
unknown.close();
}
for (SAMFileWriter writer : libraryToWriter.values()) {
writer.close();
}
return 0;
}
}