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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) 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;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMReadGroupRecord;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.metrics.MetricsFile;
import htsjdk.samtools.reference.ReferenceSequence;
import htsjdk.samtools.util.Histogram;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.Log;
import htsjdk.samtools.util.SequenceUtil;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
import org.broadinstitute.barclay.help.DocumentedFeature;
import picard.PicardException;
import picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup;
import picard.util.RExecutor;
import java.io.File;
import java.util.List;
/**
* Charts quality score distribution within a BAM file.
*
* @author Tim Fennell
*/
@CommandLineProgramProperties(
summary = QualityScoreDistribution.USAGE_SUMMARY + QualityScoreDistribution.USAGE_DETAILS,
oneLineSummary = QualityScoreDistribution.USAGE_SUMMARY,
programGroup = DiagnosticsAndQCProgramGroup.class
)
@DocumentedFeature
public class QualityScoreDistribution extends SinglePassSamProgram {
static final String USAGE_SUMMARY = "Chart the distribution of quality scores. ";
static final String USAGE_DETAILS = "This tool is used for determining the overall 'quality' for a library in a given run. To " +
"that effect, it outputs a chart and tables indicating the range of quality scores and the total numbers of bases " +
"corresponding to those scores. Options include plotting the distribution of all of the reads, only the aligned reads, " +
"or reads that have passed the Illumina Chastity filter thresholds as described " +
"here.
" +
"" +
"Note on base quality score options
" +
"If the quality score of read bases has been modified in a previous data processing step such as GATK " +
"Base Recalibration " +
"and an OQ tag is available, this tool can be set to plot the OQ value as well as the primary quality value for the " +
"evaluation.
" +
"Note: Metrics labeled as percentages are actually expressed as fractions!
" +
"Usage Example:
" +
"" +
"java -jar picard.jar QualityScoreDistribution \\
" +
" I=input.bam \\
" +
" O=qual_score_dist.txt \\
" +
" CHART=qual_score_dist.pdf" +
"" +
"
";
@Argument(shortName="CHART", doc="A file (with .pdf extension) to write the chart to.")
public File CHART_OUTPUT;
@Argument(doc="If set to true calculate mean quality over aligned reads only.")
public boolean ALIGNED_READS_ONLY = false;
@Argument(shortName="PF", doc="If set to true calculate mean quality over PF reads only.")
public boolean PF_READS_ONLY = false;
@Argument(doc="If set to true, include quality for no-call bases in the distribution.")
public boolean INCLUDE_NO_CALLS = false;
private final long[] qCounts = new long[128];
private final long[] oqCounts = new long[128];
/**
* A subtitle for the plot, usually corresponding to a library.
*/
private String plotSubtitle = "";
private final Log log = Log.getInstance(QualityScoreDistribution.class);
@Override
protected void setup(final SAMFileHeader header, final File samFile) {
IOUtil.assertFileIsWritable(OUTPUT);
IOUtil.assertFileIsWritable(CHART_OUTPUT);
// If we're working with a single library, assign that library's name
// as a suffix to the plot title
final List readGroups = header.getReadGroups();
if (readGroups.size() == 1) {
this.plotSubtitle = readGroups.get(0).getLibrary();
if (null == this.plotSubtitle) this.plotSubtitle = "";
}
}
@Override
protected void acceptRead(final SAMRecord rec, final ReferenceSequence ref) {
// Skip unwanted records
if (PF_READS_ONLY && rec.getReadFailsVendorQualityCheckFlag()) return;
if (ALIGNED_READS_ONLY && rec.getReadUnmappedFlag()) return;
if (rec.isSecondaryOrSupplementary()) return;
final byte[] bases = rec.getReadBases();
final byte[] quals = rec.getBaseQualities();
final byte[] oq = rec.getOriginalBaseQualities();
final int length = quals.length;
for (int i=0; i qHisto = new Histogram("QUALITY", "COUNT_OF_Q");
final Histogram oqHisto = new Histogram("QUALITY", "COUNT_OF_OQ");
for (int i=0; i< qCounts.length; ++i) {
if (qCounts[i] > 0) qHisto.increment( (byte) i, (double) qCounts[i]);
if (oqCounts[i] > 0) oqHisto.increment((byte) i, (double) oqCounts[i]);
}
final MetricsFile metrics = getMetricsFile();
metrics.addHistogram(qHisto);
if (!oqHisto.isEmpty()) metrics.addHistogram(oqHisto);
metrics.write(OUTPUT);
if (qHisto.isEmpty() && oqHisto.isEmpty()) {
log.warn("No valid bases found in input file. No plot will be produced.");
}
else {
// Now run R to generate a chart
final int rResult = RExecutor.executeFromClasspath(
"picard/analysis/qualityScoreDistribution.R",
OUTPUT.getAbsolutePath(),
CHART_OUTPUT.getAbsolutePath(),
INPUT.getName(),
this.plotSubtitle);
if (rResult != 0) {
throw new PicardException("R script qualityScoreDistribution.R failed with return code " + rResult);
}
}
}
}