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/*
* 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.SAMRecord;
import htsjdk.samtools.metrics.MetricBase;
import htsjdk.samtools.metrics.MetricsFile;
import htsjdk.samtools.reference.ReferenceSequence;
import htsjdk.samtools.util.IOUtil;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
import org.broadinstitute.barclay.help.DocumentedFeature;
import picard.cmdline.StandardOptionDefinitions;
import picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup;
import java.io.File;
/**
* Command line program to calibrate quality yield metrics
*
* @author Martha Borkan
*/
@CommandLineProgramProperties(
summary = CollectQualityYieldMetrics.USAGE_SUMMARY + CollectQualityYieldMetrics.USAGE_DETAILS,
oneLineSummary = CollectQualityYieldMetrics.USAGE_SUMMARY,
programGroup = DiagnosticsAndQCProgramGroup.class
)
@DocumentedFeature
public class CollectQualityYieldMetrics extends SinglePassSamProgram {
private QualityYieldMetricsCollector collector = null;
static final String USAGE_SUMMARY = "Collect metrics about reads that pass quality thresholds and Illumina-specific filters. ";
static final String USAGE_DETAILS = "This tool evaluates the overall quality of reads within a bam file containing one read group. " +
"The output indicates the total numbers of bases within a read group that pass a minimum base quality score threshold and " +
"(in the case of Illumina data) pass Illumina quality filters as described in the " +
"GATK Dictionary entry. " +
" " +
"
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 use the OQ value instead of the primary quality value for the evaluation. " +
"
" +
"Note that the default behaviour of this program changed as of November 6th 2015 to no longer include secondary and " +
"supplemental alignments in the computation. " +
"
" +
"Please see " +
"" +
"the QualityYieldMetrics documentation for details and explanations of the output metrics." +
"";
@Argument(shortName = StandardOptionDefinitions.USE_ORIGINAL_QUALITIES_SHORT_NAME,
doc = "If available in the OQ tag, use the original quality scores " +
"as inputs instead of the quality scores in the QUAL field.")
public boolean USE_ORIGINAL_QUALITIES = true;
@Argument(doc="If true, include bases from secondary alignments in metrics. Setting to true may cause double-counting " +
"of bases if there are secondary alignments in the input file.")
public boolean INCLUDE_SECONDARY_ALIGNMENTS = false;
@Argument(doc="If true, include bases from supplemental alignments in metrics. Setting to true may cause double-counting " +
"of bases if there are supplemental alignments in the input file.")
public boolean INCLUDE_SUPPLEMENTAL_ALIGNMENTS = false;
/** Ensure that we get all reads regardless of alignment status. */
@Override protected boolean usesNoRefReads() { return true; }
@Override
protected void setup(final SAMFileHeader header, final File samFile) {
IOUtil.assertFileIsWritable(OUTPUT);
this.collector = new QualityYieldMetricsCollector(USE_ORIGINAL_QUALITIES, INCLUDE_SECONDARY_ALIGNMENTS, INCLUDE_SUPPLEMENTAL_ALIGNMENTS);
}
@Override
protected void acceptRead(final SAMRecord rec, final ReferenceSequence ref) {
this.collector.acceptRecord(rec, ref);
}
@Override
protected void finish() {
final MetricsFile metricsFile = getMetricsFile();
this.collector.finish();
this.collector.addMetricsToFile(metricsFile);
metricsFile.write(OUTPUT);
}
public static class QualityYieldMetricsCollector {
// If true, include bases from secondary alignments in metrics. Setting to true may cause double-counting
// of bases if there are secondary alignments in the input file.
private final boolean useOriginalQualities;
// If true, include bases from secondary alignments in metrics. Setting to true may cause double-counting
// of bases if there are secondary alignments in the input file.
private final boolean includeSecondaryAlignments;
// If true, include bases from supplemental alignments in metrics. Setting to true may cause double-counting
// of bases if there are supplemental alignments in the input file.
public final boolean includeSupplementalAlignments;
// The metrics to be accumulated
private final QualityYieldMetrics metrics = new QualityYieldMetrics();
public QualityYieldMetricsCollector(final boolean useOriginalQualities,
final boolean includeSecondaryAlignments,
final boolean includeSupplementalAlignments) {
this.useOriginalQualities = useOriginalQualities;
this.includeSecondaryAlignments = includeSecondaryAlignments;
this.includeSupplementalAlignments = includeSupplementalAlignments;
}
public void acceptRecord(final SAMRecord rec, final ReferenceSequence ref) {
if (!this.includeSecondaryAlignments && rec.getNotPrimaryAlignmentFlag()) return;
if (!this.includeSupplementalAlignments && rec.getSupplementaryAlignmentFlag()) return;
final int length = rec.getReadLength();
metrics.TOTAL_READS++;
metrics.TOTAL_BASES += length;
final boolean isPfRead = !rec.getReadFailsVendorQualityCheckFlag();
if (isPfRead) {
metrics.PF_READS++;
metrics.PF_BASES += length;
}
final byte[] quals;
if (this.useOriginalQualities) {
byte[] tmp = rec.getOriginalBaseQualities();
if (tmp == null) tmp = rec.getBaseQualities();
quals = tmp;
} else {
quals = rec.getBaseQualities();
}
// add up quals, and quals >= 20
for (final int qual : quals) {
metrics.Q20_EQUIVALENT_YIELD += qual;
if (qual >= 30) {
metrics.Q20_BASES++;
metrics.Q30_BASES++;
} else if (qual >= 20) {
metrics.Q20_BASES++;
}
if (isPfRead) {
metrics.PF_Q20_EQUIVALENT_YIELD += qual;
if (qual >= 30) {
metrics.PF_Q20_BASES++;
metrics.PF_Q30_BASES++;
} else if (qual >= 20) {
metrics.PF_Q20_BASES++;
}
}
}
}
public void finish() {
metrics.READ_LENGTH = metrics.TOTAL_READS == 0 ? 0 : (int) (metrics.TOTAL_BASES / metrics.TOTAL_READS);
metrics.Q20_EQUIVALENT_YIELD = metrics.Q20_EQUIVALENT_YIELD / 20;
metrics.PF_Q20_EQUIVALENT_YIELD = metrics.PF_Q20_EQUIVALENT_YIELD / 20;
}
public void addMetricsToFile(final MetricsFile metricsFile) {
metricsFile.addMetric(metrics);
}
}
/** A set of metrics used to describe the general quality of a BAM file */
public static class QualityYieldMetrics extends MetricBase {
/** The total number of reads in the input file */
public long TOTAL_READS = 0;
/** The number of reads that are PF - pass filter */
public long PF_READS = 0;
/** The average read length of all the reads (will be fixed for a lane) */
public int READ_LENGTH = 0;
/** The total number of bases in all reads */
public long TOTAL_BASES;
/** The total number of bases in all PF reads */
public long PF_BASES = 0;
/** The number of bases in all reads that achieve quality score 20 or higher */
public long Q20_BASES = 0;
/** The number of bases in PF reads that achieve quality score 20 or higher */
public long PF_Q20_BASES = 0;
/** The number of bases in all reads that achieve quality score 30 or higher */
public long Q30_BASES = 0;
/** The number of bases in PF reads that achieve quality score 30 or higher */
public long PF_Q30_BASES = 0;
/** The sum of quality scores of all bases divided by 20 */
public long Q20_EQUIVALENT_YIELD = 0;
/** The sum of quality scores of all bases in PF reads divided by 20 */
public long PF_Q20_EQUIVALENT_YIELD = 0;
}
}
