GA4GHScheme.java

/*
 * The MIT License
 *
 * Copyright (c) 2015 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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 * THE SOFTWARE.
 */

package picard.vcf;

import picard.vcf.GenotypeConcordanceStates.*;

/**
 * The scheme is defined in the constructor.
 *
 * The default scheme is derived from the GA4GH Benchmarking Work Group's proposed evaluation scheme.
 *
 * In general, we are comparing two sets of alleles.  Therefore, we can have zero or more contingency table values represented in one comparison.  For example, if the truthset is
 * a heterozygous call with both alleles non-reference (HET_VAR1_VAR2), and the callset is a heterozygous call with both alleles non-reference with one of the alternate alleles
 * matching an alternate allele in the callset, we would have a true positive, false positive, and false negative.  The true positive is from the matching alternate alleles, the
 * false positive is the alternate allele found in the callset but not found in the truthset, and the false negative is the alternate in the truthset not found in the callset.
 *
 * We also include a true negative in cases where the reference allele is found in both the truthset and callset.
 *
 * We have no HET_VAR2_VAR3 case, as VAR2/VAR3 are simply symbolic, and so we can change HET_VAR2_VAR3 into the HET_VAR3_VAR4 case.
 *
 * In this (the default) scheme
 *
 * Finally, we have NA cases, which represent tuples that our code can and should not reach.
 */

public class GA4GHScheme extends GenotypeConcordanceScheme{
    @Override
    protected void initiateScheme() {
        /**          ROW STATE            MISSING       HOM_REF       HET_REF_VAR1       HET_VAR1_VAR2        HOM_VAR1        NO_CALL        LOW_GQ        LOW_DP        VC_FILTERED   GT_FILTERED   IS_MIXED    **/
        addRow(CallState.MISSING,         NA,           TN_ONLY,      TN_FN,             FN_ONLY,             FN_ONLY,        EMPTY,         EMPTY,        EMPTY,        EMPTY,        EMPTY,        EMPTY);
        addRow(CallState.HOM_REF,         TN_ONLY,      TN_ONLY,      TN_FN,             FN_ONLY,             FN_ONLY,        EMPTY,         EMPTY,        EMPTY,        EMPTY,        EMPTY,        EMPTY);
        addRow(CallState.HET_REF_VAR1,    FP_TN,        FP_TN,        TP_TN,             TP_FN,               TP_FN,          EMPTY,         EMPTY,        EMPTY,        EMPTY,        EMPTY,        EMPTY);
        addRow(CallState.HET_REF_VAR2,    NA,           NA,           FP_TN_FN,          NA,                  FP_FN,          NA,            NA,           NA,           NA,           NA,           NA);
        addRow(CallState.HET_REF_VAR3,    NA,           NA,           NA,                FP_FN,               NA,             NA,            NA,           NA,           NA,           NA,           NA);
        addRow(CallState.HET_VAR1_VAR2,   FP_ONLY,      FP_ONLY,      TP_FP,             TP_ONLY,             TP_FP_FN,       EMPTY,         EMPTY,        EMPTY,        EMPTY,        EMPTY,        EMPTY);
        addRow(CallState.HET_VAR1_VAR3,   NA,           NA,           NA,                TP_FP_FN,            NA,             NA,            NA,           NA,           NA,           NA,           NA);
        addRow(CallState.HET_VAR3_VAR4,   FP_ONLY,      FP_ONLY,      FP_FN,             FP_FN,               FP_FN,          NA,            NA,           NA,           NA,           NA,           NA);
        addRow(CallState.HOM_VAR1,        FP_ONLY,      FP_ONLY,      TP_FP,             TP_FN,               TP_ONLY,        EMPTY,         EMPTY,        EMPTY,        EMPTY,        EMPTY,        EMPTY);
        addRow(CallState.HOM_VAR2,        NA,           NA,           FP_FN,             TP_FN,               FP_FN,          NA,            NA,           NA,           NA,           NA,           NA);
        addRow(CallState.HOM_VAR3,        NA,           NA,           NA,                FP_FN,               NA,             NA,            NA,           NA,           NA,           NA,           NA);
        addRow(CallState.NO_CALL,         EMPTY,        EMPTY,        EMPTY,             EMPTY,               EMPTY,          EMPTY,         EMPTY,        EMPTY,        EMPTY,        EMPTY,        EMPTY);
        addRow(CallState.VC_FILTERED,     EMPTY,        TN_ONLY,      TN_FN,             FN_ONLY,             FN_ONLY,        EMPTY,         EMPTY,        EMPTY,        EMPTY,        EMPTY,        EMPTY);
        addRow(CallState.GT_FILTERED,     EMPTY,        TN_ONLY,      TN_FN,             FN_ONLY,             FN_ONLY,        EMPTY,         EMPTY,        EMPTY,        EMPTY,        EMPTY,        EMPTY);
        addRow(CallState.LOW_GQ,          EMPTY,        TN_ONLY,      TN_FN,             FN_ONLY,             FN_ONLY,        EMPTY,         EMPTY,        EMPTY,        EMPTY,        EMPTY,        EMPTY);
        addRow(CallState.LOW_DP,          EMPTY,        TN_ONLY,      TN_FN,             FN_ONLY,             FN_ONLY,        EMPTY,         EMPTY,        EMPTY,        EMPTY,        EMPTY,        EMPTY);
        addRow(CallState.IS_MIXED,        EMPTY,        EMPTY,        EMPTY,             EMPTY,               EMPTY,          EMPTY,         EMPTY,        EMPTY,        EMPTY,        EMPTY,        EMPTY);
    }
}