picard.analysis.GcBiasSummaryMetrics Maven / Gradle / Ivy
/*
* The MIT License
*
* Copyright (c) 2009 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
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package picard.analysis;
import picard.metrics.MultilevelMetrics;
/**
* High level metrics that capture how biased the coverage in a certain lane is.
*
* @author Tim Fennell
*/
public class GcBiasSummaryMetrics extends MultilevelMetrics {
public String ACCUMULATION_LEVEL;
/** This option is used to mark including or excluding duplicates. */
public String READS_USED;
/** The window size on the genome used to calculate the GC of the sequence. */
public int WINDOW_SIZE;
/** The total number of clusters that were seen in the gc bias calculation. */
public long TOTAL_CLUSTERS;
/** The total number of aligned reads used to compute the gc bias metrics. */
public long ALIGNED_READS;
/**
* Illumina-style AT dropout metric. Calculated by taking each GC bin independently and calculating
* (%ref_at_gc - %reads_at_gc) and summing all positive values for GC=[0..50].
*/
public double AT_DROPOUT;
/**
* Illumina-style GC dropout metric. Calculated by taking each GC bin independently and calculating
* (%ref_at_gc - %reads_at_gc) and summing all positive values for GC=[50..100].
*/
public double GC_DROPOUT;
/**
* Normalized coverage over quintile of GC content ranging from 0 - 19.
*/
public double GC_NC_0_19;
/**
* Normalized coverage over each quintile of GC content ranging from 20 - 39.
*/
public double GC_NC_20_39;
/**
* Normalized coverage over each quintile of GC content ranging from 40 - 59.
*/
public double GC_NC_40_59;
/**
* Normalized coverage over each quintile of GC content ranging from 60 - 79.
*/
public double GC_NC_60_79;
/**
* Normalized coverage over each quintile of GC content ranging from 80 - 100.
*/
public double GC_NC_80_100;
}