/*
* The MIT License
*
* Copyright (c) 2011 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 htsjdk.samtools.metrics.MetricBase;
import java.lang.Override;
import java.lang.String;
/***
* Metric for Illumina Basecalling that stores means and standard deviations on a per-barcode per-lane basis. Averages
* and means are taken over all tiles.
*/
public class IlluminaBasecallingMetrics extends MetricBase
{
/** The lane for which the metrics were calculated. */
public String LANE;
/** The barcode sequence for which the metrics were calculated. */
public String MOLECULAR_BARCODE_SEQUENCE_1;
/** The barcode name for which the metrics were calculated. */
public String MOLECULAR_BARCODE_NAME;
/** The total number of bases assigned to the index. */
public long TOTAL_BASES;
/** The total number of passing-filter bases assigned to the index. */
public long PF_BASES;
/** The total number of reads assigned to the index. */
public long TOTAL_READS;
/** The total number of passing-filter reads assigned to the index. */
public long PF_READS;
/** The total number of clusters assigned to the index. */
public long TOTAL_CLUSTERS;
/** The total number of PF clusters assigned to the index. */
public long PF_CLUSTERS;
/** The mean number of clusters per tile. */
public double MEAN_CLUSTERS_PER_TILE = 0d;
/** The standard deviation of clusters per tile. */
public double SD_CLUSTERS_PER_TILE = 0d;
/** The mean percentage of pf clusters per tile. */
public double MEAN_PCT_PF_CLUSTERS_PER_TILE = 0d;
/** The standard deviation in percentage of pf clusters per tile. */
public double SD_PCT_PF_CLUSTERS_PER_TILE = 0d;
/** The mean number of pf clusters per tile. */
public double MEAN_PF_CLUSTERS_PER_TILE = 0d;
/** The standard deviation in number of pf clusters per tile. */
public double SD_PF_CLUSTERS_PER_TILE = 0d;
@Override
public String toString() {
return String.format("IlluminaBasecallingMetric(Lane:%s,Barcode:%s,Name:%s,MEAN_CLUSTERS_PER_TILE:%s,SD_CLUSTERS_PER_TILE:%s," +
"MEAN_PCT_PF_CLUSTERS_PER_TILE:%s,SD_PCT_PF_CLUSTERS_STD_PER_TILE:%s," +
"MEAN_PF_CLUSTERS_PER_TILE:%s,SD_PF_CLUSTERS_PER_TILE:%s",
LANE
,MOLECULAR_BARCODE_SEQUENCE_1
,MOLECULAR_BARCODE_NAME
,MEAN_CLUSTERS_PER_TILE
,SD_CLUSTERS_PER_TILE
,MEAN_PCT_PF_CLUSTERS_PER_TILE
,SD_PCT_PF_CLUSTERS_PER_TILE
,MEAN_PF_CLUSTERS_PER_TILE
,SD_PF_CLUSTERS_PER_TILE);
}
}