-add basic indel metrics to variant eval

-variants need a length method (can't assume it's a SNP)!


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1324 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/refdata/AllelicVariant.java

@@ -139,5 +139,9 @@ public interface AllelicVariant extends ReferenceOrderedDatum {
      * two allelic variants, 'A' and 'T' <i>in addition</i> to the (known) reference variant 'C'). 
      * @return
      */
-    boolean isBiallelic() ;
+    boolean isBiallelic();
+
+    /** returns the length of the variant.  For SNPs this is just 1.
+     */
+    int length();
 }

java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java

@@ -161,7 +161,7 @@ public interface Genotype extends Comparable<ReferenceOrderedDatum> {
      */
   //  char getAltSnpFWD() throws IllegalStateException;
     
-
+  int length();
 
 
     /** Return actual number of observed alleles (chromosomes) in the genotype.

java/src/org/broadinstitute/sting/gatk/refdata/KGenomesSNPROD.java

@@ -45,4 +45,5 @@ public class KGenomesSNPROD extends TabularROD implements SNPCallFromGenotypes {
     public int nHetGenotypes()     { return -1; }
     public int nHomVarGenotypes()  { return -1; }
     public List<Genotype> getGenotypes() { return null; }
+    public int length() { return 1; }
 }

java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java

@@ -45,6 +45,7 @@ public class PooledEMSNPROD extends TabularROD implements SNPCallFromGenotypes {
     public List<String> getGenotype() throws IllegalStateException { throw new IllegalStateException(); }
     public int getPloidy() throws IllegalStateException { return 2; }
     public boolean isBiallelic()   { return true; }
+    public int length() { return 1; }
 
     // SNPCallFromGenotypes interface
     public int nIndividuals()      { return Integer.parseInt(this.get("EM_N")); }

java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java

@@ -362,6 +362,8 @@ public class RodGLF implements ReferenceOrderedDatum, AllelicVariant, Iterator<R
         return false;
     }
 
+    public int length() { return 1; }
+
     @Override
     public int compareTo(ReferenceOrderedDatum that) {
         return this.mLoc.compareTo(that.getLocation());

java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java

@@ -490,10 +490,15 @@ class SAMPileupRecord implements Genotype, GenotypeList, Pileup {
         return nNonref  < 2;
     }
 
-	@Override
+    @Override
-	public double getConsensusConfidence() {
+    public double getConsensusConfidence() {
-		return consensusScore;
+        return consensusScore;
-	}
+    }
+
+    @Override
+    public int length() {
+        return eventLength;
+    }
 
 	@Override
 	public boolean isIndelGenotype() {

java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java

@@ -31,6 +31,7 @@ public class SangerSNPROD extends TabularROD implements SNPCallFromGenotypes {
     public List<String> getGenotype() throws IllegalStateException { throw new IllegalStateException(); }
     public int getPloidy() throws IllegalStateException { return 2; }
     public boolean isBiallelic()   { return true; }
+    public int length() { return 1; }
 
     // SNPCallFromGenotypes interface
     public int nIndividuals()      { return -1; }

java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java

@@ -5,7 +5,9 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.util.*;
 
-public class SimpleIndelROD extends TabularROD implements Genotype {
+public class SimpleIndelROD extends TabularROD implements Genotype, AllelicVariant {
+
+    private boolean KGENOMES_FORMAT = false, checkedFormat = false;
 
     public SimpleIndelROD(String name) {
         super(name);
@@ -16,24 +18,50 @@ public class SimpleIndelROD extends TabularROD implements Genotype {
     }
 
     public List<String> getFWDAlleles() {
+        if ( is1KGFormat() )
+            return Arrays.asList(this.get("4"));
+
         String str = this.get("3");
         return Arrays.asList(str.substring(0, str.indexOf(":")));    
     }
 
     public String getFWDRefBases() { return ""; }
+    public String getAltBasesFWD() { return getFWDAlleles().get(0); }
+    public String getRefBasesFWD() { return ""; }
+    public char getRefSnpFWD() { throw new IllegalStateException("I'm an indel, not a SNP"); }
+    public char getAltSnpFWD() { throw new IllegalStateException("I'm an indel, not a SNP"); }
     public char getRef() { return 'N'; }
+    public List<String> getGenotype() { return getFWDAlleles(); }
+    public boolean isGenotype() { return false; }
     public boolean isPointGenotype() { return false; }
     public boolean isIndelGenotype() { return true; }
     public boolean isSNP() { return false; }
     public boolean isReference() { return false; }
-    public boolean isInsertion() { return this.get("3").charAt(0) == '+'; }
+    public boolean isInsertion() {
-    public boolean isDeletion() { return this.get("3").charAt(0) == '-'; }
+        if ( is1KGFormat() )
-    public boolean isIndel() { return false; }
+            return this.get("3").equals("I");
+        return this.get("3").charAt(0) == '+';
+    }
+    public boolean isDeletion() {
+        if ( is1KGFormat() )
+            return this.get("3").equals("D");
+        return this.get("3").charAt(0) == '-';
+    }
+    public boolean isIndel() { return true; }
     public double getVariantConfidence() { return 0.0; }
+    public double getVariationConfidence() { return 0.0; }
     public double getConsensusConfidence() { return 0.0; }
     public boolean isBiallelic() { return true; }
     public boolean isHom() { return false; }
     public boolean isHet() { return false; }
+    public double getHeterozygosity() { return 0.0; }
+    public double getMAF() { return 0.0; }
+    public int getPloidy() { return 2; }
+    public int length() {
+        if ( is1KGFormat() )
+             return Integer.parseInt(this.get("2"));
+        return getFWDAlleles().get(0).length();
+    }
 
     public String toString() {
         StringBuffer sb = new StringBuffer();
@@ -42,4 +70,12 @@ public class SimpleIndelROD extends TabularROD implements Genotype {
         sb.append((indel.length()-1) + "\t" + (isInsertion() ? "I" : "D") + "\t" + indel.substring(1));
         return sb.toString();
     }
+
+    private boolean is1KGFormat() {
+        if ( !checkedFormat ) {
+            checkedFormat = true;
+            KGENOMES_FORMAT = this.get("3").equals("D") || this.get("3").equals("I");
+        }
+        return KGENOMES_FORMAT;
+    }
  }

java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java

@@ -246,4 +246,6 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
 		// TODO Auto-generated method stub
 		return observed.indexOf('/')==observed.lastIndexOf('/');
 	}
+
+    public int length() { return (int)(loc.getStop() - loc.getStart() + 1); }
 }

java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java

@@ -55,6 +55,7 @@ public class rodFLT extends TabularROD implements SNPCallFromGenotypes {
     public List<String> getGenotype() throws IllegalStateException { return Arrays.asList(getAltBasesFWD()); }
     public int getPloidy() throws IllegalStateException { return 2; }
     public boolean isBiallelic()   { return true; }
+    public int length() { return 1; }
 
     // SNPCallFromGenotypes interface
     public int nIndividuals()      { return -1; }

java/src/org/broadinstitute/sting/gatk/refdata/rodGFF.java

@@ -174,4 +174,5 @@ public class rodGFF extends BasicReferenceOrderedDatum implements AllelicVariant
 
     public int getPloidy() throws IllegalStateException { return 2; }
     public boolean isBiallelic() { return true; }
+    public int length() { return 1; }
 }

java/src/org/broadinstitute/sting/gatk/refdata/rodVariants.java

@@ -169,6 +169,8 @@ public class rodVariants extends BasicReferenceOrderedDatum implements AllelicVa
         return true;
     }
 
+    public int length() { return 1; }
+
     public char getReferenceBase() { return refBase; }
 
     public int getPileupDepth() { return depth; }

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/IndelMetricsAnalysis.java

@@ -0,0 +1,64 @@
+package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
+
+import org.broadinstitute.sting.gatk.refdata.AllelicVariant;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.LocusContext;
+
+import java.util.List;
+import java.util.ArrayList;
+
+/**
+ * The Broad Institute
+ * SOFTWARE COPYRIGHT NOTICE AGREEMENT
+ * This software and its documentation are copyright 2009 by the
+ * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
+ *
+ * This software is supplied without any warranty or guaranteed support whatsoever. Neither
+ * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
+ *
+ */
+public class IndelMetricsAnalysis extends BasicVariantAnalysis implements GenotypeAnalysis, PopulationAnalysis {
+    long insertions = 0;
+    long deletions = 0;
+    int maxSize = 0;
+    long[][] sizes = new long[2][100];
+
+    public IndelMetricsAnalysis() {
+        super("indel_metrics");
+        for (int i = 0; i < 100; i++)
+            sizes[0][i] = sizes[1][i] = 0;
+    }
+
+    public String update(AllelicVariant eval, RefMetaDataTracker tracker, char ref, LocusContext context) {
+        if ( eval != null && eval.isIndel() ) {
+            if ( eval.isInsertion() )
+                insertions++;
+            else if ( eval.isDeletion() )
+                deletions++;
+            else
+                throw new RuntimeException("Variant is indel, but isn't insertion or deletion!");
+
+            if ( eval.length() < 100 ) {
+                sizes[eval.isDeletion() ? 0 : 1][eval.length()]++;
+                if ( eval.length() > maxSize )
+                    maxSize = eval.length();
+            }
+        }
+
+        return null;
+    }
+
+    public List<String> done() {
+        List<String> s = new ArrayList<String>();
+        s.add(String.format("total_deletions       %d", deletions));
+        s.add(String.format("total_insertions      %d", insertions));
+        s.add(String.format(""));
+
+        s.add("Size Distribution");
+        s.add("size\tdeletions\tinsertions");
+        for ( int i = 1; i <= maxSize; i++ )
+            s.add(String.format("%d\t%d\t\t%d", i, sizes[0][i], sizes[1][i]));
+
+        return s;
+    }
+}

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java

@@ -83,7 +83,7 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
         ArrayList<VariantAnalysis> analyses = new ArrayList<VariantAnalysis>();
 
         //
-        // Add new analyzes here!
+        // Add new analyses here!
         //
         analyses.add(new VariantCounter());
         analyses.add(new VariantDBCoverage(knownSNPDBName));
@@ -93,9 +93,10 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
         analyses.add(new HardyWeinbergEquilibrium(badHWEThreshold));
         analyses.add(new ClusterCounterAnalysis());
         analyses.add(new CallableBasesAnalysis());
+        analyses.add(new IndelMetricsAnalysis());
 
         //
-        // Filter out analyzes inappropriate for our evaluation type Population or Genotype
+        // Filter out analyses inappropriate for our evaluation type Population or Genotype
         //
         Iterator<VariantAnalysis> iter = analyses.iterator();
         while ( iter.hasNext() ) {

java/src/org/broadinstitute/sting/utils/GenotypeUtils.java

@@ -187,6 +187,11 @@ public class GenotypeUtils {
 			return false;
 		}
 
+        @Override
+        public int length() {
+            return (int)(location.getStop() - location.getStart() + 1);
+        }
+
 		@Override
 		public int compareTo(ReferenceOrderedDatum o) {
 			return location.compareTo(o.getLocation());