/*
* 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.analysis.directed;
import htsjdk.samtools.SAMReadGroupRecord;
import htsjdk.samtools.reference.ReferenceSequenceFile;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.IntervalList;
import htsjdk.samtools.util.StringUtil;
import picard.analysis.MetricAccumulationLevel;
import picard.cmdline.CommandLineProgramProperties;
import picard.cmdline.Option;
import picard.cmdline.programgroups.Metrics;
import java.io.File;
import java.util.List;
import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
/**
* Calculates a set of HS metrics from a sam or bam file. See HsMetricsCollector and CollectTargetedMetrics for more details.
*
* @author Tim Fennell
*/
@CommandLineProgramProperties(
usage = "Calculates a set of Hybrid Selection specific metrics from an aligned SAM" +
"or BAM file. If a reference sequence is provided, AT/GC dropout metrics will " +
"be calculated, and the PER_TARGET_COVERAGE option can be used to output GC and " +
"mean coverage information for every target.",
usageShort = "Calculates Hybrid Selection-specific metrics for a SAM or BAM file",
programGroup = Metrics.class
)
public class CalculateHsMetrics extends CollectTargetedMetrics<HsMetrics, HsMetricCollector> {
@Option(shortName = "BI", doc = "An interval list file that contains the locations of the baits used.", minElements=1)
public List<File> BAIT_INTERVALS;
@Option(shortName = "N", doc = "Bait set name. If not provided it is inferred from the filename of the bait intervals.", optional = true)
public String BAIT_SET_NAME;
@Override
protected IntervalList getProbeIntervals() {
for (final File file : BAIT_INTERVALS) IOUtil.assertFileIsReadable(file);
return IntervalList.fromFiles(BAIT_INTERVALS);
}
@Override
protected String getProbeSetName() {
if (BAIT_SET_NAME != null) {
return BAIT_SET_NAME;
} else {
final SortedSet<String> baitSetNames = new TreeSet<String>();
for (final File file : BAIT_INTERVALS) {
baitSetNames.add(CollectTargetedMetrics.renderProbeNameFromFile(file));
}
return StringUtil.join(".", baitSetNames);
}
}
/** Stock main method. */
public static void main(final String[] argv) {
System.exit(new CalculateHsMetrics().instanceMain(argv));
}
@Override
protected HsMetricCollector makeCollector(final Set<MetricAccumulationLevel> accumulationLevels,
final List<SAMReadGroupRecord> samRgRecords,
final ReferenceSequenceFile refFile,
final File perTargetCoverage,
final IntervalList targetIntervals,
final IntervalList probeIntervals,
final String probeSetName) {
return new HsMetricCollector(accumulationLevels, samRgRecords, refFile, perTargetCoverage, targetIntervals, probeIntervals, probeSetName);
}
}