@Override
public void performOperation() throws OperationFailedException {
BEDFile intervals = (BEDFile) this.getInputBufferForClass(BEDFile.class);
BAMFile bam = (BAMFile) this.getInputBufferForClass(BAMFile.class);
DOCMetrics metrics = (DOCMetrics) getOutputBufferForClass(DOCMetrics.class);
try {
intervals.buildIntervalsMap();
CoverageCalculator covCalc = new CoverageCalculator(bam.getFile(), intervals, false);
covCalc.setThreadCount(getPipelineOwner().getThreadCount());
int[] depthHistogram = covCalc.computeOverallCoverage();
// The depth histogram is an un-normalized raw counts of the number of bases with a certain
// read depth
// for instance, the 10th position in the list of the number of bases found with read depths =
// 10
double mean = CoverageCalculator.getMean(depthHistogram);
double[] covs = CoverageCalculator.convertCountsToProportions(depthHistogram);
int[] cutoffs = new int[] {1, 10, 15, 20, 25, 50, 100};
double[] covAboveCutoffs = new double[cutoffs.length];
for (int i = 0; i < covAboveCutoffs.length; i++) {
covAboveCutoffs[i] = covs[cutoffs[i]];
}
metrics.setMeanCoverage(mean);
metrics.setCoverageProportions(covs);
metrics.setCutoffs(cutoffs);
metrics.setFractionAboveCutoff(covAboveCutoffs);
Logger.getLogger(Pipeline.primaryLoggerName)
.info(getObjectLabel() + " Found mean depth : " + mean);
} catch (IOException e) {
e.printStackTrace();
Logger.getLogger(Pipeline.primaryLoggerName)
.warning(getObjectLabel() + " encountered IO Error : " + e.getLocalizedMessage());
throw new OperationFailedException(
"IO Error calculating coverages : " + e.getLocalizedMessage(), this);
} catch (InterruptedException e) {
e.printStackTrace();
Logger.getLogger(Pipeline.primaryLoggerName)
.warning(getObjectLabel() + " was interrupted: " + e.getLocalizedMessage());
throw new OperationFailedException(
"Interrupted calculating coverages : " + e.getLocalizedMessage(), this);
}
}
protected void parseOptions() {
FileBuffer inputBEDfb = this.getInputBufferForClass(BEDFile.class);
if (inputBEDfb != null) {
inputBED = (BEDFile) inputBEDfb;
bedFileOpt = " -t " + inputBED.getAbsolutePath();
} else {
bedFileOpt = "";
}
List<FileBuffer> inputBAMBuffers = this.getAllInputBuffersForClass(BAMFile.class);
for (FileBuffer bamBuffer : inputBAMBuffers) {
inputBAMs = inputBAMs + " -b " + bamBuffer.getAbsolutePath();
}
if (extraOptions == null || extraOptions.equals("null")) {
extraOptions = "";
}
inputBuffers = this.getAllInputBuffersForClass(BAMFile.class);
refBuf = (ReferenceFile) this.getInputBufferForClass(ReferenceFile.class);
outputVCF = (VCFFile) this.getOutputBufferForClass(VCFFile.class);
}