/*
* 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.StringUtil;
import picard.PicardException;
import picard.cmdline.CommandLineProgramProperties;
import picard.cmdline.Option;
import picard.cmdline.programgroups.Metrics;
import picard.util.RExecutor;
import java.io.File;
import java.util.Arrays;
import java.util.List;
/**
* Program to generate a data table and chart of mean quality by cycle from a
* BAM file. Works best on a single lane/run of data, but can be applied to
* merged BAMs - the output may just be a little confusing.
*
* @author Tim Fennell
*/
@CommandLineProgramProperties(
usage = "Program to generate a data table and pdf chart of " +
"mean base quality by cycle from a SAM or BAM file. Works best on a single lane/run of data, but can be applied to" +
"merged BAMs. Uses R to generate chart output.",
usageShort = "Writes mean quality by cycle for a SAM or BAM file",
programGroup = Metrics.class
)
public class MeanQualityByCycle extends SinglePassSamProgram {
@Option(shortName="CHART", doc="A file (with .pdf extension) to write the chart to.")
public File CHART_OUTPUT;
@Option(doc="If set to true, calculate mean quality over aligned reads only.")
public boolean ALIGNED_READS_ONLY = false;
@Option(doc="If set to true calculate mean quality over PF reads only.")
public boolean PF_READS_ONLY = false;
private final HistogramGenerator q = new HistogramGenerator(false);
private final HistogramGenerator oq = new HistogramGenerator(true);
/**
* A subtitle for the plot, usually corresponding to a library.
*/
private String plotSubtitle = "";
private final Log log = Log.getInstance(MeanQualityByCycle.class);
/** Required main method. */
public static void main(String[] args) {
System.exit(new MeanQualityByCycle().instanceMain(args));
}
private static class HistogramGenerator {
final boolean useOriginalQualities;
int maxLengthSoFar = 0;
double[] firstReadTotalsByCycle = new double[maxLengthSoFar];
long[] firstReadCountsByCycle = new long[maxLengthSoFar];
double[] secondReadTotalsByCycle = new double[maxLengthSoFar];
long[] secondReadCountsByCycle = new long[maxLengthSoFar];
private HistogramGenerator(final boolean useOriginalQualities) {
this.useOriginalQualities = useOriginalQualities;
}
void addRecord(final SAMRecord rec) {
final byte[] quals = (useOriginalQualities ? rec.getOriginalBaseQualities() : rec.getBaseQualities());
if (quals == null) return;
final int length = quals.length;
final boolean rc = rec.getReadNegativeStrandFlag();
ensureArraysBigEnough(length+1);
for (int i=0; i<length; ++i) {
final int cycle = rc ? length-i : i+1;
if (rec.getReadPairedFlag() && rec.getSecondOfPairFlag()) {
secondReadTotalsByCycle[cycle] += quals[i];
secondReadCountsByCycle[cycle] += 1;
}
else {
firstReadTotalsByCycle[cycle] += quals[i];
firstReadCountsByCycle[cycle] += 1;
}
}
}
private void ensureArraysBigEnough(final int length) {
if (length > maxLengthSoFar) {
firstReadTotalsByCycle = Arrays.copyOf(firstReadTotalsByCycle, length);
firstReadCountsByCycle = Arrays.copyOf(firstReadCountsByCycle, length);
secondReadTotalsByCycle = Arrays.copyOf(secondReadTotalsByCycle , length);
secondReadCountsByCycle = Arrays.copyOf(secondReadCountsByCycle, length);
maxLengthSoFar = length;
}
}
Histogram<Integer> getMeanQualityHistogram() {
final String label = useOriginalQualities ? "MEAN_ORIGINAL_QUALITY" : "MEAN_QUALITY";
final Histogram<Integer> meanQualities = new Histogram<Integer>("CYCLE", label);
int firstReadLength = 0;
for (int cycle=0; cycle < firstReadTotalsByCycle.length; ++cycle) {
if (firstReadTotalsByCycle[cycle] > 0) {
meanQualities.increment(cycle, firstReadTotalsByCycle[cycle] / firstReadCountsByCycle[cycle]);
firstReadLength = cycle;
}
}
for (int i=0; i< secondReadTotalsByCycle.length; ++i) {
if (secondReadCountsByCycle[i] > 0) {
final int cycle = firstReadLength + i;
meanQualities.increment(cycle, secondReadTotalsByCycle[i] / secondReadCountsByCycle[i]);
}
}
return meanQualities;
}
boolean isEmpty() {
return maxLengthSoFar == 0;
}
}
@Override
protected void setup(final SAMFileHeader header, final File samFile) {
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<SAMReadGroupRecord> readGroups = header.getReadGroups();
if (readGroups.size() == 1) {
plotSubtitle = StringUtil.asEmptyIfNull(readGroups.get(0).getLibrary());
}
}
@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;
q.addRecord(rec);
oq.addRecord(rec);
}
@Override
protected void finish() {
// Generate a "Histogram" of mean quality and write it to the file
final MetricsFile<?,Integer> metrics = getMetricsFile();
metrics.addHistogram(q.getMeanQualityHistogram());
if (!oq.isEmpty()) metrics.addHistogram(oq.getMeanQualityHistogram());
metrics.write(OUTPUT);
if (q.isEmpty() && oq.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/meanQualityByCycle.R",
OUTPUT.getAbsolutePath(),
CHART_OUTPUT.getAbsolutePath(),
INPUT.getName(),
plotSubtitle);
if (rResult != 0) {
throw new PicardException("R script meanQualityByCycle.R failed with return code " + rResult);
}
}
}
}