Merge pull request #1168 from broadinstitute/knoblett

Implemented MetricsCollection evaluation module

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java

@@ -335,7 +335,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                 " --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
                 " --comp:comp_genotypes " + privateTestDir + "yri.trio.gatk.ug.head.vcf";
         WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
-                1, Arrays.asList("4b9dcbce0717285e3c0c736c1bed744c"));
+                1, Arrays.asList("eaa3708d9db22fca0844a652bb73b82f"));
         executeTestParallel("testSelect1", spec);
     }
 
@@ -377,7 +377,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                            " --dbsnp " + b37dbSNP132 +
                            " --eval:evalBI " + variantEvalTestDataRoot + "ALL.20100201.chr20.bi.sites.vcf" +
                            " -noST -ST Novelty -o %s";
-        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("112bb3221688acad83f29542bfb33151"));
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("fe9dcf4933a645f55be1cb0e33497e49"));
         executeTestParallel("testEvalTrackWithoutGenotypes",spec);
     }
 
@@ -404,7 +404,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                 " --eval:evalBI " + variantEvalTestDataRoot + "ALL.20100201.chr20.bi.sites.vcf" +
                 " --eval:evalBC " + variantEvalTestDataRoot + "ALL.20100201.chr20.bc.sites.vcf" +
                 " -noST -ST Novelty -o %s";
-        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("81dcdde458c1ebb9aa35289ea8f12bc8"));
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("8dfdec264fcff9472bdee7d223fdb3ca"));
         executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
     }
 
@@ -586,7 +586,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                                         "-o %s"
                                 ),
                                 1,
-                                Arrays.asList("f8460af997436a5ce4407fefb0e2724d")
+                                Arrays.asList("af317f1ea1b80e5d4bc4f2d8523ef73d")
                               );
         executeTest("testModernVCFWithLargeIndels", spec);
     }

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java

@@ -32,6 +32,7 @@ import htsjdk.samtools.SAMSequenceRecord;
 import org.apache.log4j.Logger;
 import htsjdk.tribble.Feature;
 import org.broadinstitute.gatk.engine.walkers.*;
+import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.*;
 import org.broadinstitute.gatk.utils.commandline.*;
 import org.broadinstitute.gatk.engine.CommandLineGATK;
 import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
@@ -39,7 +40,6 @@ import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection;
 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.evaluators.VariantEvaluator;
 import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.IntervalStratification;
 import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.VariantStratifier;
 import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.manager.StratificationManager;
@@ -609,7 +609,34 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
         for ( final EvaluationContext nec : stratManager.values() )
             for ( final VariantEvaluator ve : nec.getVariantEvaluators() )
                 ve.finalizeEvaluation();
-        
+
+        //send data to MetricsCollection
+        CompOverlap compOverlap = null;
+        IndelSummary indelSummary = null;
+        CountVariants countVariants = null;
+        MultiallelicSummary multiallelicSummary = null;
+        TiTvVariantEvaluator tiTvVariantEvaluator = null;
+        MetricsCollection metricsCollection = null;
+        for(final EvaluationContext nec: stratManager.values()) {
+            for(final VariantEvaluator ve : nec.getVariantEvaluators()) {
+                if (ve instanceof CompOverlap)
+                    compOverlap = (CompOverlap) ve;
+                else if (ve instanceof IndelSummary)
+                    indelSummary = (IndelSummary) ve;
+                else if (ve instanceof CountVariants)
+                    countVariants = (CountVariants) ve;
+                else if (ve instanceof MultiallelicSummary)
+                    multiallelicSummary = (MultiallelicSummary) ve;
+                else if (ve instanceof TiTvVariantEvaluator)
+                    tiTvVariantEvaluator = (TiTvVariantEvaluator) ve;
+                else if (ve instanceof MetricsCollection)
+                    metricsCollection = (MetricsCollection) ve;
+            }
+
+        if(metricsCollection != null)
+            metricsCollection.setData(compOverlap.concordantRate, indelSummary.n_SNPs, countVariants.nSNPs, indelSummary.n_indels, multiallelicSummary.nIndels, indelSummary.insertion_to_deletion_ratio, countVariants.insertionDeletionRatio, tiTvVariantEvaluator.tiTvRatio);
+        }
+
         VariantEvalReportWriter.writeReport(out, stratManager, stratManager.getStratifiers(), stratManager.get(0).getVariantEvaluators());
     }
 

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MetricsCollection.java

@@ -0,0 +1,67 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* 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 org.broadinstitute.gatk.tools.walkers.varianteval.evaluators;
+
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint;
+
+/**
+ * Created by knoblett on 9/15/15.
+ */
+
+@Analysis(description = "Metrics Collection")
+public class MetricsCollection extends VariantEvaluator {
+
+    @DataPoint(description = "The concordance rate from CompOverlap", format = "%.2f")
+    public double concordantRate;
+    @DataPoint(description = "Number of SNPs from IndelSummary", format = "%d")
+    public int nSNPs;
+    @DataPoint(description = "Number of SNP loci from CountVariants", format = "%d")
+    public long nSNPloci;
+    @DataPoint(description = "Number of indels from IndelSummary", format = "%d")
+    public int nIndels;
+    @DataPoint(description = "Number of indel loci from MultiallelicSummary", format = "%d")
+    public int nIndelLoci;
+    @DataPoint(description = "Insertion  to deletion ratio from IndelSummary")
+    public String indelRatio;
+    @DataPoint(description = "Insertion to deletion ratio from CountVariants", format = "%.2f")
+    public double indelRatioLociBased;
+    @DataPoint(description = "The transition to transversion ratio from TiTvVariantEvaluator", format = "%.2f")
+    public double tiTvRatio;
+
+    public int getComparisonOrder() {return 2;}
+
+    public void setData(double concordantRate, int nSNPs, long nSNPloci, int nIndels, int nIndelLoci, String indelRatio, double indelRatioLociBased, double tiTvRatio){
+        this.concordantRate = concordantRate;
+        this.nSNPs = nSNPs;
+        this.nSNPloci = nSNPloci;
+        this.nIndels = nIndels;
+        this.nIndelLoci = nIndelLoci;
+        this.indelRatio = indelRatio;
+        this.indelRatioLociBased = indelRatioLociBased;
+        this.tiTvRatio = tiTvRatio;
+    }
+}

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/VariantEvalUtils.java

@@ -176,6 +176,11 @@ public class VariantEvalUtils {
             }
         }
 
+        //add MetricsCollection if required modules are included
+
+        if(evals.contains(classMap.get("CompOverlap")) && evals.contains(classMap.get("IndelSummary")) && evals.contains(classMap.get("TiTvVariantEvaluator")) && evals.contains(classMap.get("CountVariants")) && evals.contains(classMap.get("MultiallelicSummary")) )
+            evals.add(classMap.get("MetricsCollection"));
+
         return evals;
     }