private void saveResults(
final MetricsFile<?, Integer> metrics,
final SAMFileHeader readsHeader,
final String inputFileName) {
MetricsUtils.saveMetrics(metrics, out, getAuthHolder());
if (metrics.getAllHistograms().isEmpty()) {
logger.warn("No valid bases found in input file.");
} else if (chartOutput != null) {
// Now run R to generate a chart
// If we're working with a single library, assign that library's name
// as a suffix to the plot title
final List<SAMReadGroupRecord> readGroups = readsHeader.getReadGroups();
/*
* A subtitle for the plot, usually corresponding to a library.
*/
String plotSubtitle = "";
if (readGroups.size() == 1) {
plotSubtitle = StringUtil.asEmptyIfNull(readGroups.get(0).getLibrary());
}
final RScriptExecutor executor = new RScriptExecutor();
executor.addScript(new Resource(MeanQualityByCycle.R_SCRIPT, MeanQualityByCycle.class));
executor.addArgs(out, chartOutput.getAbsolutePath(), inputFileName, plotSubtitle);
executor.exec();
}
}
