BatchMerge - AlleleVCF --> AllelesVCF, this (combined with Eric's fix) will solve James P.'s forum issue.

After viewing results on real case/control data from RAW -- it's really working quite well. ReadIndels, however, needs to use a T-test rather than a U-test, especially in deep coverage (at indel sites, the reads with indels will have mostly the same number of CIGAR indel elements -- one -- which doesn't really play nicely with the UTest when sample sets are large). Modified ReadsLargeInsertSize to be a two-way test (e.g. ReadsLarge and ReadsSmall). BaseQualityScore also suffers from the same issue as read indels, so switching over to a T-test in that case as well.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5653 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/RAWSampleStats.java

@@ -56,6 +56,7 @@ public class RAWSampleStats extends LocusWalker<MapHolder,RegionalAssociationHan
                 if ( ! first ) {
                     contextBuf.append(";");
                 } else {
+                    contextBuf.append("\t");
                     first = false;
                 }
                 contextBuf.append(entry.getKey().getId());

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/BaseQualityScore.java

@@ -25,4 +25,5 @@ public class BaseQualityScore extends ValueTest {
     }
 
     public boolean usePreviouslySeenReads() { return true; }
+    public boolean useTStatistic() { return true; }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/MismatchRate.java

@@ -52,6 +52,7 @@ public class MismatchRate extends ValueTest {
         Object stats = sampleStats.get(sample.getId());
         double mn;
         double std;
+        double mmr = calcMMR(pileup);
         if ( stats instanceof Pair ) {
             mn = ((Pair<Double,Double>)stats).first;
             std = ((Pair<Double,Double>)stats).second;
@@ -62,10 +63,10 @@ public class MismatchRate extends ValueTest {
             if ( std <= 0.0 ) {
                 std = 1.0;
             }
-            ra.add(pileup.size());
+            ra.add(mmr);
         }
 
-        return Arrays.asList((Number) ((calcMMR(pileup) - mn) / std));
+        return Arrays.asList((Number) ((mmr - mn) / std));
     }
 
     public double calcMMR(ReadBackedPileup rbp) {

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/ReadIndels.java

@@ -32,4 +32,5 @@ public class ReadIndels extends ValueTest {
     }
 
     public boolean usePreviouslySeenReads() { return false; }
+    public boolean useTStatistic() { return true; }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/ReadsAberrantInsertSize.java

@@ -13,9 +13,10 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
  * Time: 3:31 PM
  * To change this template use File | Settings | File Templates.
  */
-public class ReadsLargeInsertSize extends ProportionTest {
+public class ReadsAberrantInsertSize extends ProportionTest {
 
-    private int THRESHOLD;
+    private int HI_THRESHOLD;
+    private int LO_THRESHOLD;
 
     @Override
     public Pair<Number,Number> map(ReadBackedPileup rbp) {
@@ -24,7 +25,7 @@ public class ReadsLargeInsertSize extends ProportionTest {
         for (PileupElement e : rbp ) {
             if ( e.getRead().getReadPairedFlag() ) {
                 ++total;
-                if ( e.getRead().getInferredInsertSize() > THRESHOLD ) {
+                if ( e.getRead().getInferredInsertSize() > HI_THRESHOLD || e.getRead().getInferredInsertSize() < LO_THRESHOLD ) {
                     ++wonky;
                 }
             }
@@ -35,7 +36,8 @@ public class ReadsLargeInsertSize extends ProportionTest {
 
     public void init(RegionalAssociationWalker parent) {
         super.init(parent);
-        THRESHOLD = 150;
+        HI_THRESHOLD = 200;
+	LO_THRESHOLD = 50;
     }
 
     public boolean usePreviouslySeenReads() { return false; }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/ReadsWithIndels.java

@@ -0,0 +1,31 @@
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules.casecontrol;
+
+import net.sf.samtools.CigarOperator;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: chartl
+ * Date: 4/15/11
+ * Time: 12:54 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class ReadsWithIndels extends ProportionTest {
+
+    public Pair<Number,Number> map(ReadBackedPileup pileup) {
+        int numReads = 0;
+        int numWithIndels = 0;
+        for ( PileupElement e : pileup ) {
+            ++numReads;
+            if ( e.getRead().getCigar().getCigarElements().contains(CigarOperator.DELETION) || e.getRead().getCigar().getCigarElements().contains(CigarOperator.INSERTION)) {
+                ++numWithIndels;
+            }
+        }
+
+        return new Pair<Number,Number>(numWithIndels,numReads);
+    }
+
+    public boolean usePreviouslySeenReads() { return false; }
+}

scala/qscript/playground/BatchMerge.q

@@ -53,7 +53,7 @@ class batchMergePipeline extends QScript {
         this.baq = BAQ.CalculationMode.CALCULATE_AS_NECESSARY
       }
       this.intervals :+= extractIntervals.listOut
-      this.alleleVCF = combineVCFs.outVCF
+      this.allelesVCF = combineVCFs.outVCF
       this.jarFile = new File(stingDir+"/dist/GenomeAnalysisTK.jar")
       this.memoryLimit = 4
       this.scatterCount = 60