/*
* The MIT License
*
* Copyright (c) 2010 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 htsjdk.samtools.metrics.MetricBase;
/**
* Summary fingerprinting metrics and statistics about the comparison of the sequence data
* from a single read group (lane or index within a lane) vs. a set of known genotypes for
* the expected sample.
*
* @author Tim Fennell
*/
public class FingerprintingSummaryMetrics extends MetricBase {
/** The read group from which sequence data was drawn for comparison. */
public String READ_GROUP;
/** The sample whose known genotypes the sequence data was compared to. */
public String SAMPLE;
/** The Log Likelihood of the sequence data given the expected sample's genotypes. */
public double LL_EXPECTED_SAMPLE;
/** The Log Likelihood of the sequence data given a random sample from the human population. */
public double LL_RANDOM_SAMPLE;
/**
* The LOD for Expected Sample vs. Random Sample. A positive LOD indicates that the sequence data
* is more likely to come from the expected sample vs. a random sample from the population, by LOD logs.
* I.e. a value of 6 indicates that the sequence data is 1,000,000 more likely to come from the expected
* sample than from a random sample. A negative LOD indicates the reverse - that the sequence data is more
* likely to come from a random sample than from the expected sample.
*/
public double LOD_EXPECTED_SAMPLE;
/** The number of haplotypes that had expected genotypes to compare to. */
public int HAPLOTYPES_WITH_GENOTYPES;
/**
* The subset of genotyped haplotypes for which there was sufficient sequence data to
* confidently genotype the haplotype. Note: all haplotypes with sequence coverage contribute to the
* LOD score, even if they cannot be "confidently checked" individually.
* */
public int HAPLOTYPES_CONFIDENTLY_CHECKED;
/** The subset of confidently checked haplotypes that match the expected genotypes. */
public int HAPLOTYPES_CONFIDENTLY_MATCHING;
/** num of hets, observed as homs with LOD > threshold */
public int HET_AS_HOM;
/** num of homs, observed as hets with LOD > threshold */
public int HOM_AS_HET;
/** num of homs, observed as other homs with LOD > threshold */
public int HOM_AS_OTHER_HOM;
}