From 089ae85be7d4e2a459eb481ed59ca33abc5d3c01 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 27 Jul 2009 17:36:59 +0000
Subject: [PATCH] 1. output grep-able strings for genotype eval 2. free DB
 coverage from isSNP restriction

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1322 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../varianteval/GenotypeConcordance.java        | 17 ++++++++++++-----
 .../walkers/varianteval/VariantDBCoverage.java  |  6 ++----
 2 files changed, 14 insertions(+), 9 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java
index 7bc645ebe..b4c6d8fe1 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java
@@ -94,7 +94,7 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
             StringBuffer sb = new StringBuffer();
             sb.append(TRUTH_NAMES[i] + "\t");
             for (int j=0; j < 4; j++)
-                sb.append(cellToString(table[i][j], truth_totals[i]) + "\t\t");
+                sb.append(table[i][j] +" (" + cellPercent(table[i][j], truth_totals[i]) + ")\t\t");
             sb.append(truth_totals[i]);
             s.add(sb.toString());
         }
@@ -104,21 +104,28 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
             StringBuffer sb = new StringBuffer();
             sb.append(TRUTH_NAMES[i] + "\t");
             for (int j=0; j < 4; j++)
-                sb.append(cellToString(table[i][j], truth_totals[i]) + "\t\t");
+                sb.append(table[i][j] + " (" + cellPercent(table[i][j], calls_totals[j]) + ")\t\t");
             s.add(sb.toString());
         }
         s.add(String.format("TOTALS\t%d\t\t%d\t\t%d\t\t%d", calls_totals[CALL_REF], calls_totals[CALL_VAR_HET], calls_totals[CALL_VAR_HOM], calls_totals[NO_CALL]));
+        s.add("\n");
+        for (int i=0; i < 4; i++) {
+            for (int j=0; j < 4; j++) {
+                s.add(TRUTH_NAMES[i]+"_"+CALL_NAMES[j]+"_COUNT "+table[i][j]);
+                s.add(TRUTH_NAMES[i]+"_"+CALL_NAMES[j]+"_PERCENT_OF_TRUTH "+cellPercent(table[i][j], truth_totals[i]));
+                s.add(TRUTH_NAMES[i]+"_"+CALL_NAMES[j]+"_PERCENT_OF_CALLS "+cellPercent(table[i][j], calls_totals[j]));
+            }
+        }
         return s;
     }
 
-    private static String cellToString(int count, int total) {
+    private static String cellPercent(int count, int total) {
         StringBuffer sb = new StringBuffer();
-        sb.append(count + " (");
         if ( total == 0 )
             sb.append(0);
         else
             sb.append(100*count/total);
-        sb.append("%)");
+        sb.append("%");
         return sb.toString();
     }
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantDBCoverage.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantDBCoverage.java
index 20b2cab4c..11a9bab79 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantDBCoverage.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantDBCoverage.java
@@ -4,9 +4,7 @@ import org.broadinstitute.sting.gatk.refdata.AllelicVariant;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.LocusContext;
 
-import java.io.PrintStream;
 import java.util.List;
-import java.util.Arrays;
 import java.util.ArrayList;
 
 /**
@@ -53,8 +51,8 @@ public class VariantDBCoverage extends BasicVariantAnalysis implements GenotypeA
     public String update(AllelicVariant eval, RefMetaDataTracker tracker, char ref, LocusContext context) {
         // There are four cases here:
         AllelicVariant dbsnp = (AllelicVariant)tracker.lookup(dbName, null);
-        inc(dbsnp != null, eval != null && eval.isSNP());
-        return dbsnp == null && eval != null && eval.isSNP() ? "Novel " + eval : null;
+        inc(dbsnp != null, eval != null);
+        return dbsnp == null && eval != null ? "Novel " + eval : null;
     }
 
     /**