/*
* The MIT License
*
* Copyright (c) 2016 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
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*
* The above copyright notice and this permission notice shall be included in
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*
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package picard.vcf.MendelianViolations;
import picard.analysis.MergeableMetricBase;
import picard.pedigree.Sex;
/**
* Describes the type and number of mendelian violations found within a Trio.
*/
public class MendelianViolationMetrics extends MergeableMetricBase {
public static String getExtension() {
return "mendelian_violation_metrics";
}
/** The family ID assigned to the trio for which these metrics are calculated.*/
@MergeByAssertEquals
public String FAMILY_ID;
/** The ID of the mother within the trio.*/
@MergeByAssertEquals
public String MOTHER;
/** The ID of the father within the trio.*/
@MergeByAssertEquals
public String FATHER;
/** The ID of the offspring within the trio.*/
@MergeByAssertEquals
public String OFFSPRING;
/** The sex of the offspring. */
@MergeByAssertEquals
public Sex OFFSPRING_SEX = null;
/** The number of biallelic, SNP sites at which all relevant samples exceeded the minimum genotype quality and depth and at least one of the samples was variant. */
@MergeByAdding
public long NUM_VARIANT_SITES;
/** The number of diploid sites at which a potential de-novo mutation was observed (i.e. both parents are hom-ref, offspring is not hom-ref. */
@MergeByAdding
public long NUM_DIPLOID_DENOVO;
/** The number of sites at which both parents are homozygous for a non-reference allele and the offspring is heterozygous. */
@MergeByAdding
public long NUM_HOMVAR_HOMVAR_HET;
/** The number of sites at which the one parent is homozygous reference, the other homozygous variant and the offspring is homozygous. */
@MergeByAdding
public long NUM_HOMREF_HOMVAR_HOM;
/** The number of sites at which one parent is homozygous, the other is heterozygous and the offspring is the alternative homozygote. */
@MergeByAdding
public long NUM_HOM_HET_HOM;
/** The number of sites at which the offspring is haploid, the parent is homozygous reference and the offspring is non-reference. */
@MergeByAdding
public long NUM_HAPLOID_DENOVO;
/** The number of sites at which the offspring is haploid and exhibits a reference allele that is not present in the parent. */
@MergeByAdding
public long NUM_HAPLOID_OTHER;
/** The number of otherwise unclassified events. */
@MergeByAdding
public long NUM_OTHER;
/** The total of all mendelian violations observed. */
@NoMergingIsDerived
public long TOTAL_MENDELIAN_VIOLATIONS;
@Override
public void calculateDerivedFields() {
TOTAL_MENDELIAN_VIOLATIONS = NUM_DIPLOID_DENOVO + NUM_HOMVAR_HOMVAR_HET +
NUM_HOMREF_HOMVAR_HOM + NUM_HOM_HET_HOM + NUM_HAPLOID_DENOVO +
NUM_HAPLOID_OTHER + NUM_OTHER;
}
}