@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);
}
}
