public static File writePhasingMetrics(
final Map<Integer, ? extends Collection<Tile>> laneTiles,
final File outputDirectory,
final String outputPrefix,
final MetricsFile<MetricBase, Comparable<?>> phasingMetricsFile) {
laneTiles
.entrySet()
.stream()
.forEach(
entry ->
IlluminaPhasingMetrics.getPhasingMetricsForTiles(
entry.getKey().longValue(), entry.getValue())
.forEach(phasingMetricsFile::addMetric));
return writeMetrics(
phasingMetricsFile, outputDirectory, outputPrefix, IlluminaPhasingMetrics.getExtension());
}
/**
* Calculate the median phasing & prephasing values for a lane's tiles and create the appropriate
* IlluminaPhasingMetrics for them
*/
public static Collection<IlluminaPhasingMetrics> getPhasingMetricsForTiles(
final long lane, final Collection<Tile> tilesForLane) {
final LanePhasingMetricsCollector lanePhasingMetricsCollector =
new LanePhasingMetricsCollector(tilesForLane);
final Collection<IlluminaPhasingMetrics> phasingMetrics =
new ArrayList<IlluminaPhasingMetrics>();
for (final TileTemplateRead tileTemplateRead :
lanePhasingMetricsCollector.getMedianPhasingMap().keySet()) {
final IlluminaPhasingMetrics phasingMetric = new IlluminaPhasingMetrics();
phasingMetric.LANE = lane;
phasingMetric.TYPE_NAME = tileTemplateRead.toString();
phasingMetric.PHASING_APPLIED =
lanePhasingMetricsCollector.getMedianPhasingMap().get(tileTemplateRead);
phasingMetric.PREPHASING_APPLIED =
lanePhasingMetricsCollector.getMedianPrePhasingMap().get(tileTemplateRead);
phasingMetrics.add(phasingMetric);
}
return phasingMetrics;
}