picard.analysis.FingerprintingDetailMetrics Maven / Gradle / Ivy
/*
* 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
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* THE SOFTWARE.
*/
package picard.analysis;
import htsjdk.samtools.metrics.MetricBase;
/**
* Detailed metrics about an individual SNP/Haplotype comparison within a fingerprint comparison.
*
* @author Tim Fennell
*/
public class FingerprintingDetailMetrics extends MetricBase {
/** The sequencing read group from which sequence data was fingerprinted. */
public String READ_GROUP;
/** The name of the sample who's genotypes the sequence data was compared to. */
public String SAMPLE;
/**
* The name of a representative SNP within the haplotype that was compared. Will usually be the
* exact SNP that was genotyped externally.
*/
public String SNP;
/** The possible alleles for the SNP. */
public String SNP_ALLELES;
/** The chromosome on which the SNP resides. */
public String CHROM;
/** The position of the SNP on the chromosome. */
public int POSITION;
/** The expected genotype of the sample at the SNP locus. */
public String EXPECTED_GENOTYPE;
/** The most likely genotype given the observed evidence at the SNP locus in the sequencing data. */
public String OBSERVED_GENOTYPE;
/** The LOD score for OBSERVED_GENOTYPE vs. the next most likely genotype in the sequencing data. */
public double LOD;
/** The number of observations of the first, or A, allele of the SNP in the sequencing data. */
public int OBS_A;
/** The number of observations of the second, or B, allele of the SNP in the sequencing data. */
public int OBS_B;
}