picard.illumina.IlluminaPhasingMetrics Maven / Gradle / Ivy
/*
* The MIT License
*
* Copyright (c) 2014 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package picard.illumina;
import picard.illumina.parser.Tile;
import picard.illumina.parser.TileTemplateRead;
import htsjdk.samtools.metrics.MetricBase;
import java.lang.String;import java.util.ArrayList;
import java.util.Collection;
/**
* Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis.
* Phasing refers to the fraction of molecules that fall behind or jump ahead (prephasing) during a read cycle.
* For each lane/template read # (i.e. FIRST, SECOND) combination we will store the median values of both the phasing and prephasing
* values for every tile in that lane/template read pair.
*
* @author jgentry
*/
public class IlluminaPhasingMetrics extends MetricBase {
/** Illumina flowcell lane number */
public long LANE;
/** Defines an Illumina template read number (first or second) */
public String TYPE_NAME;
/** Median phasing value across all tiles in a lane, applied to the first and second template reads */
public double PHASING_APPLIED;
/** Median pre-phasing value across all tiles in a lane, applied to the first and second template reads */
public double PREPHASING_APPLIED;
/** Calculate the median phasing & prephasing values for a lane's tiles and create the appropriate IlluminaPhasingMetrics for them */
public static Collection getPhasingMetricsForTiles(final long lane, final Collection tilesForLane) {
final LanePhasingMetricsCollector lanePhasingMetricsCollector = new LanePhasingMetricsCollector(tilesForLane);
final Collection phasingMetrics = new ArrayList();
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;
}
/** This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection. */
public static String getExtension() {
return "illumina_phasing_metrics";
}
}