/*
* The MIT License
*
* Copyright (c) 2013 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.analysis;
import picard.metrics.MultilevelMetrics;
/**
* Holds summary statistics from RRBS processing QC
*
* @author jgentry
*/
public final class RrbsSummaryMetrics extends MultilevelMetrics {
/** Number of mapped reads processed */
public Integer READS_ALIGNED;
/** Number of times a non-CpG cytosine was encountered */
public Integer NON_CPG_BASES;
/** Number of times a non-CpG cytosine was converted (C->T for +, G->A for -) */
public Integer NON_CPG_CONVERTED_BASES;
/** NON_CPG_BASES / NON_CPG_CONVERTED_BASES */
public Double PCT_NON_CPG_BASES_CONVERTED;
/** Number of CpG sites encountered */
public Integer CPG_BASES_SEEN;
/** Number of CpG sites that were converted (TG for +, CA for -) */
public Integer CPG_BASES_CONVERTED;
/** CPG_BASES_SEEN / CPG_BASES_CONVERTED */
public Double PCT_CPG_BASES_CONVERTED;
/** Mean coverage of CpG sites */
public Double MEAN_CPG_COVERAGE;
/** Median coverage of CpG sites */
public Integer MEDIAN_CPG_COVERAGE;
/** Number of reads discarded for having no CpG sites */
public Integer READS_WITH_NO_CPG;
/** Number of reads discarded due to being too short */
public Integer READS_IGNORED_SHORT;
/** Number of reads discarded for exceeding the mismatch threshold */
public Integer READS_IGNORED_MISMATCHES;
}