2prev

mikessh · Apr 5, 2015 · 69996ab · 69996ab
1 parent bde5662
commit 69996ab
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/src/main/groovy/com/antigenomics/vdjtools/overlap/OverlapEvaluator.groovy b/src/main/groovy/com/antigenomics/vdjtools/overlap/OverlapEvaluator.groovy
@@ -128,7 +128,7 @@ class OverlapEvaluator {
                 def div1 = jointSample.getSample(i).diversity,
                         div2 = jointSample.getSample(j).diversity,
                         div12 = jointSample.getIntersectionDiv(i, j)
-                return 1.0 - div12 / (div1 + div2 - div12)
+                return div12 / (div1 + div2 - div12)
 
         /*
          case ChaoSorensen:
@@ -186,7 +186,7 @@ class OverlapEvaluator {
                     Dy += y * y
                 }
 
-                return 1.0 - 2 * xy / (Dx + Dy)
+                return 2 * xy / (Dx + Dy)
 
             case vJSD:
                 return MathUtil.JSD(

diff --git a/src/main/groovy/com/antigenomics/vdjtools/overlap/OverlapMetricNormalization.groovy b/src/main/groovy/com/antigenomics/vdjtools/overlap/OverlapMetricNormalization.groovy
@@ -58,6 +58,8 @@ public enum OverlapMetricNormalization {
                 return -Math.log10(x + 1e-9)
             case R:
                 return (1.0 - x) / 2
+            case Index:
+                return 1.0 - x
         }
         x
     }