/*
* The MIT License
*
* Copyright (c) 2010 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.SAMFileReader;
import htsjdk.samtools.SAMFileWriter;
import htsjdk.samtools.SAMFileWriterFactory;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.ValidationStringency;
import htsjdk.samtools.util.CloseableIterator;
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 = CleanSam.USAGE,
usageShort = CleanSam.USAGE,
programGroup = SamOrBam.class
)
public class CleanSam extends CommandLineProgram {
static final String USAGE = "Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads";
@Option(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "Input SAM to be cleaned.")
public File INPUT;
@Option(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "Where to write cleaned SAM.")
public File OUTPUT;
public static void main(final String[] argv) {
new CleanSam().instanceMainWithExit(argv);
}
/**
* Do the work after command line has been parsed.
* RuntimeException may be thrown by this method, and are reported appropriately.
*
* @return program exit status.
*/
@Override
protected int doWork() {
IOUtil.assertFileIsReadable(INPUT);
IOUtil.assertFileIsWritable(OUTPUT);
final ValidationStringency originalStringency = SAMFileReader.getDefaultValidationStringency();
if (VALIDATION_STRINGENCY == ValidationStringency.STRICT) {
SAMFileReader.setDefaultValidationStringency(ValidationStringency.LENIENT);
}
try {
final SAMFileReader reader = new SAMFileReader(INPUT);
final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), true, OUTPUT);
final CloseableIterator<SAMRecord> it = reader.iterator();
final ProgressLogger progress = new ProgressLogger(Log.getInstance(CleanSam.class));
// If the read (or its mate) maps off the end of the alignment, clip it
while(it.hasNext()) {
final SAMRecord rec = it.next();
// If the read (or its mate) maps off the end of the alignment, clip it
AbstractAlignmentMerger.createNewCigarsIfMapsOffEndOfReference(rec);
// check the read's mapping quality
if (rec.getReadUnmappedFlag() && 0 != rec.getMappingQuality()) {
rec.setMappingQuality(0);
}
writer.addAlignment(rec);
progress.record(rec);
}
writer.close();
it.close();
}
finally {
SAMFileReader.setDefaultValidationStringency(originalStringency);
}
return 0;
}
}