/*
* 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.SAMRecord;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.Log;
import htsjdk.samtools.util.ProgressLogger;
import picard.PicardException;
import picard.cmdline.CommandLineProgram;
import picard.cmdline.CommandLineProgramProperties;
import picard.cmdline.Option;
import picard.cmdline.StandardOptionDefinitions;
import picard.cmdline.programgroups.SamOrBam;
import java.io.File;
/**
* Converts a BAM file to human-readable SAM output or vice versa
*
* @author ktibbett@broadinstitute.org
*/
@CommandLineProgramProperties(
usage = "Convert a BAM file to a SAM file, or SAM to BAM.\n" +
"Input and output formats are determined by file extension.",
usageShort = "Convert a BAM file to a SAM file, or a SAM to a BAM",
programGroup = SamOrBam.class
)
public class
SamFormatConverter extends CommandLineProgram {
private static final String PROGRAM_VERSION = "1.0";
// The following attributes define the command-line arguments
@Option(doc="The BAM or SAM file to parse.", shortName= StandardOptionDefinitions.INPUT_SHORT_NAME) public File INPUT;
@Option(doc="The BAM or SAM output file. ", shortName=StandardOptionDefinitions.OUTPUT_SHORT_NAME) public File OUTPUT;
public static void main(final String[] argv) {
new SamFormatConverter().instanceMainWithExit(argv);
}
protected int doWork() {
IOUtil.assertFileIsReadable(INPUT);
IOUtil.assertFileIsWritable(OUTPUT);
final SAMFileReader reader = new SAMFileReader(INPUT);
final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), true, OUTPUT);
if (CREATE_INDEX && writer.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate){
throw new PicardException("Can't CREATE_INDEX unless sort order is coordinate");
}
final ProgressLogger progress = new ProgressLogger(Log.getInstance(SamFormatConverter.class));
for (final SAMRecord rec : reader) {
writer.addAlignment(rec);
progress.record(rec);
}
reader.close();
writer.close();
return 0;
}
}