/*
* 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.SAMFileWriter;
import htsjdk.samtools.SAMFileWriterFactory;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import htsjdk.samtools.util.CloserUtil;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.Log;
import htsjdk.samtools.util.ProgressLogger;
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;
/**
* @author alecw@broadinstitute.org
*/
@CommandLineProgramProperties(
usage = SortSam.USAGE_SUMMARY + SortSam.USAGE_DETAILS,
usageShort = SortSam.USAGE_SUMMARY,
programGroup = SamOrBam.class
)
public class SortSam extends CommandLineProgram {
static final String USAGE_SUMMARY = "Sorts a SAM or BAM file. ";
static final String USAGE_DETAILS = "This tool sorts the input SAM or BAM file by coordinate, queryname (QNAME), or some other property " +
"of the SAM record. The SortOrder of a SAM/BAM file is found in the SAM file header tag @HD in the field labeled SO. " +
"" +
"<p>For a coordinate sorted SAM/BAM file, read alignments are sorted first by the reference sequence name (RNAME) field using the " +
"reference sequence dictionary (@SQ tag). Alignments within these subgroups are secondarily sorted using the left-most mapping " +
"position of the read (POS). Subsequent to this sorting scheme, alignments are listed arbitrarily.</p>" +
"" +
"For queryname-sorted alignments, all alignments are grouped using the queryname field but the alignments are not necessarily sorted within these groups. " +
"Reads having the same queryname are derived from the same template. " +
"<h4>Usage example:</h4>" +
"<pre>" +
"java -jar picard.jar SortSam \\<br />" +
" I=input.bam \\<br />" +
" O=sorted.bam \\<br />" +
" SORT_ORDER=coordinate" +
"</pre>" +
"<hr />";
@Option(doc = "The BAM or SAM file to sort.", shortName = StandardOptionDefinitions.INPUT_SHORT_NAME)
public File INPUT;
@Option(doc = "The sorted BAM or SAM output file. ", shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME)
public File OUTPUT;
@Option(shortName = StandardOptionDefinitions.SORT_ORDER_SHORT_NAME, doc = "Sort order of output file")
public SAMFileHeader.SortOrder SORT_ORDER;
private final Log log = Log.getInstance(SortSam.class);
public static void main(final String[] argv) {
new SortSam().instanceMainWithExit(argv);
}
protected int doWork() {
IOUtil.assertFileIsReadable(INPUT);
IOUtil.assertFileIsWritable(OUTPUT);
final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT);
;
reader.getFileHeader().setSortOrder(SORT_ORDER);
final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), false, OUTPUT);
writer.setProgressLogger(
new ProgressLogger(log, (int) 1e7, "Wrote", "records from a sorting collection"));
final ProgressLogger progress = new ProgressLogger(log, (int) 1e7, "Read");
for (final SAMRecord rec : reader) {
writer.addAlignment(rec);
progress.record(rec);
}
log.info("Finished reading inputs, merging and writing to output now.");
CloserUtil.close(reader);
writer.close();
return 0;
}
}