@Override
protected void finish() {
multiCollector.finish();
final MetricsFile<InsertSizeMetrics, Integer> file = getMetricsFile();
multiCollector.addAllLevelsToFile(file);
if (file.getNumHistograms() == 0) {
// can happen if user sets MINIMUM_PCT = 0.5, etc.
log.warn(
"All data categories were discarded because they contained < "
+ MINIMUM_PCT
+ " of the total aligned paired data.");
final InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector allReadsCollector =
(InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector)
multiCollector.getAllReadsCollector();
log.warn(
"Total mapped pairs in all categories: "
+ (allReadsCollector == null
? allReadsCollector
: allReadsCollector.getTotalInserts()));
} else {
file.write(OUTPUT);
final int rResult;
if (HISTOGRAM_WIDTH == null) {
rResult =
RExecutor.executeFromClasspath(
HISTOGRAM_R_SCRIPT,
OUTPUT.getAbsolutePath(),
HISTOGRAM_FILE.getAbsolutePath(),
INPUT.getName());
} else {
rResult =
RExecutor.executeFromClasspath(
HISTOGRAM_R_SCRIPT,
OUTPUT.getAbsolutePath(),
HISTOGRAM_FILE.getAbsolutePath(),
INPUT.getName(),
String.valueOf(
HISTOGRAM_WIDTH)); // HISTOGRAM_WIDTH is passed because R automatically sets
// histogram width to the last
// bin that has data, which may be less than HISTOGRAM_WIDTH and confuse the user.
}
if (rResult != 0) {
throw new PicardException(
"R script " + HISTOGRAM_R_SCRIPT + " failed with return code " + rResult);
}
}
}
@Override
protected void acceptRead(final SAMRecord record, final ReferenceSequence ref) {
multiCollector.acceptRecord(record, ref);
}