From d6a0b65ac954bd6bc6d1bd8a6fdf676c8d084549 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 11 Sep 2009 16:23:01 +0000
Subject: [PATCH] Changes:

Rollback of Variant-related changes of r1585, additional PGC code




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1586 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/refdata/AllelicVariant.java       |  4 ----
 .../sting/gatk/refdata/PooledEMSNPROD.java       |  1 -
 .../sting/gatk/refdata/RodGLF.java               |  4 ----
 .../sting/gatk/refdata/RodGeliText.java          |  1 -
 .../sting/gatk/refdata/RodGenotypeChipAsGFF.java |  1 -
 .../sting/gatk/refdata/SangerSNPROD.java         |  1 -
 .../sting/gatk/refdata/SimpleIndelROD.java       |  1 -
 .../sting/gatk/refdata/rodDbSNP.java             |  1 -
 .../varianteval/PooledGenotypeConcordance.java   | 16 ++++++++++++++++
 9 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/AllelicVariant.java b/java/src/org/broadinstitute/sting/gatk/refdata/AllelicVariant.java
index 78e34f136..86720d95e 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/AllelicVariant.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/AllelicVariant.java
@@ -145,8 +145,4 @@ public interface AllelicVariant extends ReferenceOrderedDatum {
      */
     int length();
 
-    /**
-     * returns TRUE if the variant is one for pooled calls, FALSE if it is not
-     */
-    boolean isPooled();
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java
index 36f4ebc1b..d3f44faa0 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java
@@ -46,7 +46,6 @@ public class PooledEMSNPROD extends TabularROD implements SNPCallFromGenotypes {
     public int getPloidy() throws IllegalStateException { return 2; }
     public boolean isBiallelic()   { return true; }
     public int length() { return 1; }
-    public boolean isPooled() { return true; }
 
     // SNPCallFromGenotypes interface
     public int nIndividuals()      { return Integer.parseInt(this.get("EM_N")); }
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java
index b54b6f46a..1f6cc3120 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java
@@ -408,9 +408,5 @@ public class RodGLF implements ReferenceOrderedDatum, AllelicVariant, Iterator<R
         return glf;
     }
 
-    @Override
-    public boolean isPooled() {
-        return false;
-    }
 }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java
index bcfa43aeb..2974e0bb4 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java
@@ -171,7 +171,6 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements AllelicVa
         return true;
     }
 
-    public boolean isPooled() { return false; }
 
     public int length() { return 1; }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodGenotypeChipAsGFF.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodGenotypeChipAsGFF.java
index f0f1f036b..3f8107700 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodGenotypeChipAsGFF.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RodGenotypeChipAsGFF.java
@@ -175,5 +175,4 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
     public int getPloidy() throws IllegalStateException { return 2; }
     public boolean isBiallelic() { return true; }
     public int length() { return 1; }
-    public boolean isPooled() { return false; }
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java
index 22c98546e..3e71e0457 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java
@@ -32,7 +32,6 @@ public class SangerSNPROD extends TabularROD implements SNPCallFromGenotypes {
     public int getPloidy() throws IllegalStateException { return 2; }
     public boolean isBiallelic()   { return true; }
     public int length() { return 1; }
-    public boolean isPooled() { return false; }
 
     // SNPCallFromGenotypes interface
     public int nIndividuals()      { return -1; }
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java
index ef4279a0d..85579645d 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java
@@ -58,7 +58,6 @@ public class SimpleIndelROD extends TabularROD implements Genotype, AllelicVaria
     public double getHeterozygosity() { return 0.0; }
     public double getMAF() { return 0.0; }
     public int getPloidy() { return 2; }
-    public boolean isPooled() { return false; }
     public int length() {
         if ( is1KGFormat() )
              return Integer.parseInt(this.get("2"));
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
index 874fd5908..0c4a25c2c 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
@@ -240,5 +240,4 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
 
     public int length() { return (int)(loc.getStop() - loc.getStart() + 1); }
 
-    public boolean isPooled() { return false; }
 }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledGenotypeConcordance.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledGenotypeConcordance.java
index 3806d5f11..cedcec7e2 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledGenotypeConcordance.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledGenotypeConcordance.java
@@ -80,7 +80,23 @@ public class PooledGenotypeConcordance extends BasicVariantAnalysis implements G
 
     public void inc(AllelicVariant eval, RefMetaDataTracker tracker, char ref, AlignmentContext context, int pool, int nameOffset) {
         AllelicVariant chip = (AllelicVariant) tracker.lookup(individualsByPool[pool][nameOffset],null);
+        if( (chip != null && !chip.isGenotype()) || ! isCorrectVariantType(eval)) {
+            String errMsg = "Trying to compare non-pooled data or non-genotype data."
+            throw new StingException(errMsg);
+        }
 
+        int truthIndex, callIndex;
+        if(chip == null) {
+            truthIndex = UNKNOWN;
+        } else if(chip.isReference()) // todo -- how do we want to do pooled concordance checking?
+
+    }
+
+    public boolean isCorrectVariantType(AllelicVariant eval) {
+        // todo -- this. Check if eval is a TypeOf some ROD class that's the right pooled call output that we
+        // todo -- want to deal with. For now this will work
+
+        return eval.isPooled();
     }