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A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
/*
* The MIT License
*
* Copyright (c) 2018 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.*;
import htsjdk.samtools.util.*;
import htsjdk.tribble.annotation.Strand;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
import org.broadinstitute.barclay.help.DocumentedFeature;
import picard.PicardException;
import picard.cmdline.CommandLineProgram;
import picard.cmdline.StandardOptionDefinitions;
import picard.cmdline.programgroups.ReadDataManipulationProgramGroup;
import java.io.File;
import java.io.IOException;
import java.util.List;
import java.util.Optional;
@CommandLineProgramProperties(
summary = AddOATag.USAGE_DETAILS,
oneLineSummary = AddOATag.USAGE_SUMMARY,
programGroup = ReadDataManipulationProgramGroup.class)
@DocumentedFeature
public class AddOATag extends CommandLineProgram {
static final String USAGE_SUMMARY = "Record current alignment information to OA tag.";
static final String USAGE_DETAILS = "This tool takes in an aligned SAM or BAM and adds the " +
"OA tag to every aligned read unless an interval list is specified, where it only adds the tag to reads " +
"that fall within the intervals in the interval list. This can be useful if you are about to realign but want " +
"to keep the original alignment information as a separate tag." +
"
"+
"Usage example:
" +
"" +
"java -jar picard.jar AddOATag \\
" +
" L=some_picard.interval_list \\
" +
" I=sorted.bam \\
" +
" O=fixed.bam
"+
"";
@Argument(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "SAM or BAM input file")
public String INPUT;
@Argument(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "SAM or BAM file to write merged result to")
public String OUTPUT;
@Argument(shortName = "L", doc = "If provided, only records that overlap given interval list will have the OA tag added.", optional = true)
public File INTERVAL_LIST;
private static final Log log = Log.getInstance(AddOATag.class);
@Override
protected int doWork() {
try (final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(IOUtil.getPath(INPUT));
final SAMFileWriter writer = new SAMFileWriterFactory().makeWriter(reader.getFileHeader(), true, IOUtil.getPath(OUTPUT), REFERENCE_SEQUENCE)) {
writer.setProgressLogger(
new ProgressLogger(log, (int) 1e7, "Wrote", "records"));
final OverlapDetector overlapDetector = getOverlapDetectorFromIntervalListFile(INTERVAL_LIST, 0, 0);
for (final SAMRecord rec : reader) {
if (overlapDetector == null || overlapDetector.overlapsAny(rec)) {
setOATag(rec);
}
writer.addAlignment(rec);
}
} catch (IOException e) {
log.error(e);
return 1;
}
return 0;
}
// Take an interval list file and convert it to an overlap detector, can add left and right padding
static OverlapDetector getOverlapDetectorFromIntervalListFile(final File intervalList, final int lhsBuffer, final int rhsBuffer) {
if (intervalList == null) {
return null;
}
List intervals = IntervalList.fromFile(intervalList).uniqued().getIntervals();
OverlapDetector detector = new OverlapDetector<>(lhsBuffer, rhsBuffer);
detector.addAll(intervals, intervals);
return detector;
}
// format OA tag string according to the spec
//TODO: Move this to htsjdk once https://github.com/samtools/hts-specs/pull/193 is merged
private void setOATag(SAMRecord rec) {
if (rec.getReferenceName().contains(",")) {
throw new PicardException(String.format("Reference name for record %s contains a comma character.", rec.getReadName()));
}
final String oaValue;
if (rec.getReadUnmappedFlag()) {
oaValue = String.format("*,0,%s,*,255,;", rec.getReadNegativeStrandFlag() ? Strand.NEGATIVE : Strand.POSITIVE);
} else {
oaValue = String.format("%s,%s,%s,%s,%s,%s;",
rec.getReferenceName(),
rec.getAlignmentStart(),
rec.getReadNegativeStrandFlag() ? Strand.NEGATIVE : Strand.POSITIVE,
rec.getCigarString(),
rec.getMappingQuality(),
Optional.ofNullable(rec.getAttribute(SAMTag.NM.name())).orElse(""));
}
rec.setAttribute(SAMTag.OA.name(), Optional.ofNullable(rec.getAttribute(SAMTag.OA.name())).orElse("") + oaValue);
}
}