/**
* Constructor takes a lane's collection of Tiles and calculates the median phasing/prephasing for
* the first and second (if available) reads
*/
public LanePhasingMetricsCollector(final Collection<Tile> laneTiles) {
final Map<TileTemplateRead, Float> medianPhasingMapLocal =
new TreeMap<TileTemplateRead, Float>();
final Map<TileTemplateRead, Float> medianPrePhasingMapLocal =
new TreeMap<TileTemplateRead, Float>();
final CollectionUtil.MultiMap<TileTemplateRead, Float> phasingValues =
new CollectionUtil.MultiMap<TileTemplateRead, Float>();
final CollectionUtil.MultiMap<TileTemplateRead, Float> prePhasingValues =
new CollectionUtil.MultiMap<TileTemplateRead, Float>();
// Collect the phasing/prephasing values from all of the tiles, sorted by template read #
for (final Tile tile : laneTiles) {
for (final TileTemplateRead tileTemplateRead : tile.getPhasingMap().keySet()) {
phasingValues.append(tileTemplateRead, tile.getPhasingMap().get(tileTemplateRead));
prePhasingValues.append(tileTemplateRead, tile.getPrePhasingMap().get(tileTemplateRead));
}
}
// Calculate the medians for the collected data
for (final TileTemplateRead tileTemplateRead : phasingValues.keySet()) {
medianPhasingMapLocal.put(
tileTemplateRead, medianPercentage(phasingValues.get(tileTemplateRead)));
medianPrePhasingMapLocal.put(
tileTemplateRead, medianPercentage(prePhasingValues.get(tileTemplateRead)));
}
this.medianPhasingMap = Collections.unmodifiableMap(medianPhasingMapLocal);
this.medianPrePhasingMap = Collections.unmodifiableMap(medianPrePhasingMapLocal);
}
private static double calculateLaneDensityFromTiles(final Collection<Tile> tiles) {
double area = 0;
double clusters = 0;
for (final Tile tile : tiles) {
area += (tile.getClusterCount() / tile.getClusterDensity());
clusters += tile.getClusterCount();
}
return clusters / area;
}