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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) 2016 Nils Homer
*
* 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;
import htsjdk.samtools.SAMReadGroupRecord;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.metrics.MetricsFile;
import htsjdk.samtools.util.Histogram;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.IntervalList;
import htsjdk.samtools.util.Log;
import htsjdk.samtools.util.StringUtil;
import org.broadinstitute.barclay.argparser.ExperimentalFeature;
import org.broadinstitute.barclay.help.DocumentedFeature;
import picard.PicardException;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
import picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup;
import picard.filter.CountingFilter;
import picard.filter.CountingPairedFilter;
import picard.util.RExecutor;
import java.io.File;
import java.util.List;
@DocumentedFeature
@ExperimentalFeature
@CommandLineProgramProperties(
summary = CollectWgsMetricsWithNonZeroCoverage.USAGE_SUMMARY + CollectWgsMetricsWithNonZeroCoverage.USAGE_DETAILS,
oneLineSummary = CollectWgsMetricsWithNonZeroCoverage.USAGE_SUMMARY,
programGroup = DiagnosticsAndQCProgramGroup.class
)
public class CollectWgsMetricsWithNonZeroCoverage extends CollectWgsMetrics {
static final String USAGE_SUMMARY = "Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments. ";
static final String USAGE_DETAILS = "This tool collects metrics about the percentages of reads that pass base- and mapping- quality " +
"filters as well as coverage (read-depth) levels. Both minimum base- and mapping-quality values as well as the maximum " +
"read depths (coverage cap) are user defined. This extends CollectWgsMetrics by including metrics related only to sites" +
"with non-zero (>0) coverage." +
"Note: Metrics labeled as percentages are actually expressed as fractions!
" +
"Usage Example:
" +
"" +
"java -jar picard.jar CollectWgsMetricsWithNonZeroCoverage \\
" +
" I=input.bam \\
"+
" O=collect_wgs_metrics.txt \\
" +
" CHART=collect_wgs_metrics.pdf \\
" +
" R=reference_sequence.fasta " +
"" +
"Please see the " +
"" +
"WgsMetricsWithNonZeroCoverage documentation for detailed explanations of the output metrics." +
"
";
@Argument(shortName = "CHART", doc = "A file (with .pdf extension) to write the chart to.")
public File CHART_OUTPUT;
private final Log log = Log.getInstance(CollectWgsMetricsWithNonZeroCoverage.class);
// Store this here since we need access to it in the doWork method
private WgsMetricsWithNonZeroCoverageCollector collector = null;
private SamReader samReader = null;
/** Metrics for evaluating the performance of whole genome sequencing experiments. */
public static class WgsMetricsWithNonZeroCoverage extends WgsMetrics {
public enum Category { WHOLE_GENOME, NON_ZERO_REGIONS }
/** One of either WHOLE_GENOME or NON_ZERO_REGIONS */
@MergeByAssertEquals
public Category CATEGORY;
public WgsMetricsWithNonZeroCoverage() {
super();
}
public WgsMetricsWithNonZeroCoverage(final IntervalList intervals,
final Histogram highQualityDepthHistogram,
final Histogram unfilteredDepthHistogram,
final double pctExcludedByMapq,
final double pctExcludedByDupes,
final double pctExcludedByPairing,
final double pctExcludedByBaseq,
final double pctExcludedByOverlap,
final double pctExcludedByCapping,
final double pctTotal,
final int coverageCap,
final Histogram unfilteredBaseQHistogram,
final int sampleSize) {
super(intervals, highQualityDepthHistogram, unfilteredDepthHistogram, pctExcludedByMapq, pctExcludedByDupes, pctExcludedByPairing, pctExcludedByBaseq,
pctExcludedByOverlap, pctExcludedByCapping, pctTotal, coverageCap, unfilteredBaseQHistogram, sampleSize);
}
}
public static void main(final String[] args) {
new CollectWgsMetrics().instanceMainWithExit(args);
}
@Override
protected SamReader getSamReader() {
if (this.samReader == null) {
this.samReader = super.getSamReader();
}
return this.samReader;
}
@Override
protected int doWork() {
IOUtil.assertFileIsWritable(CHART_OUTPUT);
IOUtil.assertFileIsReadable(INPUT);
// Initialize the SamReader, so the header is available prior to super.doWork, for getIntervalsToExamine call. */
getSamReader();
this.collector = new WgsMetricsWithNonZeroCoverageCollector(this, COVERAGE_CAP, getIntervalsToExamine());
super.doWork();
final List readGroups = getSamFileHeader().getReadGroups();
final String plotSubtitle = (readGroups.size() == 1) ? StringUtil.asEmptyIfNull(readGroups.get(0).getLibrary()) : "";
if (collector.areHistogramsEmpty()) {
log.warn("No valid bases found in input file. No plot will be produced.");
} else {
final int rResult = RExecutor.executeFromClasspath("picard/analysis/wgsHistogram.R",
OUTPUT.getAbsolutePath(),
CHART_OUTPUT.getAbsolutePath(),
INPUT.getName(),
plotSubtitle);
if (rResult != 0) {
throw new PicardException("R script wgsHistogram.R failed with return code " + rResult);
}
}
return 0;
}
@Override
protected WgsMetrics generateWgsMetrics(final IntervalList intervals,
final Histogram highQualityDepthHistogram,
final Histogram unfilteredDepthHistogram,
final double pctExcludedByMapq,
final double pctExcludedByDupes,
final double pctExcludedByPairing,
final double pctExcludedByBaseq,
final double pctExcludedByOverlap,
final double pctExcludedByCapping,
final double pctTotal,
final int coverageCap,
final Histogram unfilteredBaseQHistogram,
final int sampleSize) {
return new WgsMetricsWithNonZeroCoverage(
intervals,
highQualityDepthHistogram,
unfilteredDepthHistogram,
pctExcludedByMapq,
pctExcludedByDupes,
pctExcludedByPairing,
pctExcludedByBaseq,
pctExcludedByOverlap,
pctExcludedByCapping,
pctTotal,
coverageCap,
unfilteredBaseQHistogram,
sampleSize);
}
@Override
protected WgsMetricsCollector getCollector(final int coverageCap, final IntervalList intervals) {
assert(coverageCap == this.collector.coverageCap);
return this.collector;
}
protected class WgsMetricsWithNonZeroCoverageCollector extends WgsMetricsCollector {
Histogram highQualityDepthHistogram;
Histogram highQualityDepthHistogramNonZero;
public WgsMetricsWithNonZeroCoverageCollector(final CollectWgsMetricsWithNonZeroCoverage metrics,
final int coverageCap, final IntervalList intervals) {
super(metrics, coverageCap, intervals);
}
@Override
public void addToMetricsFile(final MetricsFile file,
final boolean includeBQHistogram,
final CountingFilter dupeFilter,
final CountingFilter mapqFilter,
final CountingPairedFilter pairFilter) {
highQualityDepthHistogram = getDepthHistogram();
highQualityDepthHistogramNonZero = getDepthHistogramNonZero();
// calculate metrics the same way as in CollectWgsMetrics
final WgsMetricsWithNonZeroCoverage metrics = (WgsMetricsWithNonZeroCoverage) getMetrics(dupeFilter, mapqFilter, pairFilter);
metrics.CATEGORY = WgsMetricsWithNonZeroCoverage.Category.WHOLE_GENOME;
// set count of the coverage-zero bin to 0 and re-calculate metrics
// note we don't need to update the base quality histogram; there are no bases in the depth = 0 bin
highQualityDepthHistogramArray[0] = 0;
unfilteredDepthHistogramArray[0] = 0;
final WgsMetricsWithNonZeroCoverage metricsNonZero = (WgsMetricsWithNonZeroCoverage) getMetrics(dupeFilter, mapqFilter, pairFilter);
metricsNonZero.CATEGORY = WgsMetricsWithNonZeroCoverage.Category.NON_ZERO_REGIONS;
file.addMetric(metrics);
file.addMetric(metricsNonZero);
file.addHistogram(highQualityDepthHistogram);
file.addHistogram(highQualityDepthHistogramNonZero);
if (includeBQHistogram) {
addBaseQHistogram(file);
}
}
protected Histogram getDepthHistogram() {
return getHistogram(highQualityDepthHistogramArray, "coverage", "count_WHOLE_GENOME");
}
private Histogram getDepthHistogramNonZero() {
final Histogram depthHistogram = new Histogram<>("coverage", "count_NON_ZERO_REGIONS");
// do not include the zero-coverage bin
for (int i = 1; i < highQualityDepthHistogramArray.length; ++i) {
depthHistogram.increment(i, highQualityDepthHistogramArray[i]);
}
return depthHistogram;
}
public boolean areHistogramsEmpty() {
return (highQualityDepthHistogram.isEmpty() || highQualityDepthHistogramNonZero.isEmpty());
}
}
}