/*
* 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.util;
import picard.cmdline.CommandLineProgram;
import picard.cmdline.CommandLineProgramProperties;
import picard.cmdline.programgroups.Intervals;
import picard.cmdline.Option;
import picard.cmdline.StandardOptionDefinitions;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.liftover.LiftOver;
import htsjdk.samtools.util.Interval;
import htsjdk.samtools.util.IntervalList;
import htsjdk.samtools.util.Log;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMFileReader;
import java.io.File;
import java.lang.Override;import java.lang.String;import java.util.List;
/**
* @author alecw@broadinstitute.org
*/
@CommandLineProgramProperties(
usage = "Lifts over an interval list from one reference build to another. Based on UCSC liftOver." +
" Uses a UCSC chain file to guide the liftOver.",
usageShort = "Lifts over an interval list from one reference build to another",
programGroup = Intervals.class
)
public class LiftOverIntervalList extends CommandLineProgram {
private static final Log LOG = Log.getInstance(LiftOverIntervalList.class);
@Option(doc = "Interval list to be lifted over.", shortName = StandardOptionDefinitions.INPUT_SHORT_NAME)
public File INPUT;
@Option(doc = "Where to write lifted-over interval list.", shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME)
public File OUTPUT;
@Option(doc = "Sequence dictionary to write into the output interval list.",
shortName = StandardOptionDefinitions.SEQUENCE_DICTIONARY_SHORT_NAME)
public File SEQUENCE_DICTIONARY;
@Option(doc = "Chain file that guides LiftOver.")
public File CHAIN;
@Option(doc = "Minimum percentage of bases in each input interval that must map to output interval.")
public double MIN_LIFTOVER_PCT = LiftOver.DEFAULT_LIFTOVER_MINMATCH;
public static void main(final String[] argv) {
new LiftOverIntervalList().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.assertFileIsReadable(SEQUENCE_DICTIONARY);
IOUtil.assertFileIsReadable(CHAIN);
IOUtil.assertFileIsWritable(OUTPUT);
final LiftOver liftOver = new LiftOver(CHAIN);
liftOver.setLiftOverMinMatch(MIN_LIFTOVER_PCT);
final IntervalList fromIntervals = IntervalList.fromFile(INPUT);
final SAMFileHeader toHeader = new SAMFileReader(SEQUENCE_DICTIONARY).getFileHeader();
liftOver.validateToSequences(toHeader.getSequenceDictionary());
final IntervalList toIntervals = new IntervalList(toHeader);
boolean anyFailed = false;
for (final Interval fromInterval : fromIntervals) {
final Interval toInterval = liftOver.liftOver(fromInterval);
if (toInterval != null) {
toIntervals.add(toInterval);
} else {
anyFailed = true;
LOG.warn("Liftover failed for ", fromInterval, "(len ", fromInterval.length(), ")");
final List<LiftOver.PartialLiftover> partials = liftOver.diagnosticLiftover(fromInterval);
for (final LiftOver.PartialLiftover partial : partials) {
LOG.info(partial);
}
}
}
toIntervals.sort();
toIntervals.write(OUTPUT);
return anyFailed? 1: 0;
}
}