Ti/Tv by AC

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3252 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java

@@ -57,7 +57,7 @@ public class GenotypeConcordance extends VariantEvaluator {
     @DataPoint(description = "the variant quality score histograms for true positive and false positive calls")
     QualityScoreHistograms qualityScoreHistograms = null;
 
-    private static final int MAX_MISSED_VALIDATION_DATA = 10000;
+    private static final int MAX_MISSED_VALIDATION_DATA = 100;
 
 
     class FrequencyStats implements TableType {

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java

@@ -0,0 +1,161 @@
+package org.broadinstitute.sting.gatk.walkers.varianteval;
+
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
+import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
+import org.broadinstitute.sting.playground.utils.report.utils.TableType;
+import org.broadinstitute.sting.utils.StingException;
+import java.util.ArrayList;
+
+/*
+ * 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 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.
+ */
+
+/**
+ * @author depristo
+ * @since Apr 11, 2010
+ */
+
+@Analysis(name = "Quality Metrics by allele count", description = "Shows various stats binned by allele count")
+public class SimpleMetricsByAC extends VariantEvaluator {
+    // a mapping from quality score histogram bin to Ti/Tv ratio
+    @DataPoint(name="TiTv by AC", description = "TiTv by allele count")
+    MetricsByAc metrics = null;
+
+    //@DataPoint(name="Quality by Allele Count", description = "average variant quality for each allele count")
+    //AlleleCountStats alleleCountStats = null;
+
+    private final static Object[] METRIC_COLUMNS = {"AC", "nTi", "nTv", "n", "Ti/Tv"};
+
+    class MetricsAtAC {
+        public int ac = -1, nTi = 0, nTv = 0;
+
+        public MetricsAtAC(int ac) { this.ac = ac; }
+
+        public void update(VariantContext eval) {
+            if ( eval.isTransition() )
+                nTi++;
+            else
+                nTv++;
+        }
+
+        // corresponding to METRIC_COLUMNS
+        public String getColumn(int i) {
+            switch (i) {
+                case 0: return String.valueOf(ac);
+                case 1: return String.valueOf(nTi);
+                case 2: return String.valueOf(nTv);
+                case 3: return String.valueOf(nTi + nTv);
+                case 4: return String.valueOf(ratio(nTi, nTv));
+                default:
+                    throw new StingException("Unexpected column " + i);
+            }
+        }
+    }
+
+    class MetricsByAc implements TableType {
+        int nchromosomes = -1;
+        ArrayList<MetricsAtAC> metrics = new ArrayList<MetricsAtAC>();
+        Object[] rows = null;
+
+        public MetricsByAc( int nchromosomes ) {
+            this.nchromosomes = nchromosomes;
+            rows = new Object[nchromosomes+1];
+            metrics = new ArrayList<MetricsAtAC>(nchromosomes+1);
+            for ( int i = 0; i < nchromosomes + 1; i++ ) {
+                metrics.add(new MetricsAtAC(i));
+                rows[i] = "ac" + i;
+            }
+        }
+
+        public Object[] getRowKeys() {
+            return rows;
+        }
+
+        public Object[] getColumnKeys() {
+            return METRIC_COLUMNS;
+        }
+
+        public String getName() {
+            return "MetricsByAc";
+        }
+
+        //
+        public String getCell(int ac, int y) {
+            return metrics.get(ac).getColumn(y);
+        }
+
+        public String toString() {
+            String returnString = "";
+            return returnString;
+        }
+
+        public void incrValue( VariantContext eval ) {
+            int an = eval.getChromosomeCount();
+            if ( an == nchromosomes ) { // ignore sites with no calls
+                int ac = eval.getChromosomeCount(eval.getAlternateAllele(0));
+                metrics.get(ac).update(eval);
+            }
+        }
+    }
+
+    public SimpleMetricsByAC(VariantEvalWalker parent) {
+        // don't do anything
+    }
+
+    public String getName() {
+        return "SimpleMetricsByAC";
+    }
+
+    public int getComparisonOrder() {
+        return 1;   // we only need to see each eval track
+    }
+
+    public boolean enabled() {
+        return true;
+    }
+
+    public String toString() {
+        return getName();
+    }
+
+    public String update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        final String interesting = null;
+
+        if (eval != null && eval.isSNP() && eval.hasGenotypes() ) {
+            if ( metrics == null )
+                metrics = new MetricsByAc(2 * eval.getNSamples());
+            metrics.incrValue(eval);
+        }
+
+        return interesting; // This module doesn't capture any interesting sites, so return null
+    }
+
+    //public void finalizeEvaluation() {
+    //
+    //}
+}

java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java

@@ -7,7 +7,8 @@ import java.util.Arrays;
 import java.util.HashMap;
 import java.util.Map;
 
-public class VariantEvalIntegrationTest extends WalkerTest {
+public class
+        VariantEvalIntegrationTest extends WalkerTest {
     private static String cmdRoot = "-T VariantEval" +
             " -R " + oneKGLocation + "reference/human_b36_both.fasta -reportType Grep";
 
@@ -19,8 +20,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
     @Test
     public void testVESimple() {
         HashMap<String, String> expectations = new HashMap<String, String>();
-        expectations.put("-L 1:1-10,000,000", "b28ffcff420177d9b73aa726e260fb34");
+        expectations.put("-L 1:1-10,000,000", "f2ce1e0e9bbe81b482a9448cb88e2263");
-        expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "749d53687497d7939713e9ce586642a4");
+        expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "b39229f55b726c2f61a17463a3c883be");
 
         for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
             String extraArgs = entry.getKey();
@@ -41,10 +42,10 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                 " -B comp_hapmap,VCF," + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
 
 
-        String matchingMD5 = "3abf37ada16619f4b3f39cb7ecad497f";
+        String matchingMD5 = "f8c7bd3ce4499cff485d2170ce896af9";
         expectations.put("", matchingMD5);
         expectations.put(" -known comp_hapmap -known dbsnp", matchingMD5);
-        expectations.put(" -known comp_hapmap", "75026dbdad38f74ac697a7c102e64db4");
+        expectations.put(" -known comp_hapmap", "99c687b95b1a4614cd76570bfd24e7a6");
 
         for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
             String extraArgs2 = entry.getKey();
@@ -62,7 +63,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
         String extraArgs = "-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 30";
         WalkerTestSpec spec = new WalkerTestSpec( root + " " + extraArgs + " -o %s -outputVCF %s",
                 2,
-                Arrays.asList("06cdbe7f94990dfe61b5e3ec03b49151", "b4a42c90318adc88361691ece50426f2"));
+                Arrays.asList("bfbad4053c89c264cec16040df0bcc4c", "b4a42c90318adc88361691ece50426f2"));
         executeTest("testVEWriteVCF", spec);
     }
 }