/*
* Copyright 2012-2015 Broad Institute, Inc.
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* obtaining a copy of this software and associated documentation
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* 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.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators;

import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis;
import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint;
import htsjdk.variant.variantcontext.VariantContext;

@Analysis(name = "PrintMissingComp", description = "the overlap between eval and comp sites")
public class PrintMissingComp extends VariantEvaluator {
    @DataPoint(description = "number of eval sites outside of comp sites", format = "%d")
    public long nMissing = 0;

    public String getName() {
        return "PrintMissingComp";
    }

    public int getComparisonOrder() {
        return 2;   // we need to see each eval track and each comp track
    }

    public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
        final boolean compIsGood = comp != null && comp.isNotFiltered() && comp.isSNP();
        final boolean evalIsGood = eval != null && eval.isSNP();

        if ( compIsGood & ! evalIsGood ) {
            nMissing++;
            super.getWalker().getLogger().info("MissingFrom" + eval.toString() + " is missing from " + comp.getSource());
        }
    }
}