From f3e4c24f63f1e843d8fdf4d4cc95756dc2383b8e Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 28 Mar 2011 22:22:37 +0000
Subject: [PATCH] Framework works properly now, but whitening still has a kink
 which is that the covariance matrix gets re-sorted automatically by the
 eigendecomposition, so somehow the association between eigenvalue and
 dimension (e.g. association track) needs to be maintained throughout.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5530 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../association/RegionalAssociationRecalibrator.java        | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/RegionalAssociationRecalibrator.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/RegionalAssociationRecalibrator.java
index 4e6ab7785..c704c9041 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/RegionalAssociationRecalibrator.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/RegionalAssociationRecalibrator.java
@@ -136,10 +136,12 @@ public class RegionalAssociationRecalibrator extends RodWalker<RegionalAssociati
         Arrays.sort(normRanks);
         for ( LocHashingPair lhp : normByLoc ) {
             int rank = Arrays.binarySearch(normRanks,lhp.second);
+            // note - equal values will always be assigned the same rank -- however
+            // it is proper, no need for random assignment.
             double prob = ((double) rank)/((double)normRanks.length);
             int qual = AssociationTestRunner.pToQ(prob);
-            out.printf("%s\t%d\t%d\t%d\t%.2e\t%d",lhp.getFirst().getContig(),lhp.getFirst().getStart(),lhp.getFirst().getStop(),
-                    qual,prob,rank);
+            out.printf("%s\t%d\t%d\t%d\t%.2e\t%d\t%.2e%n",lhp.getFirst().getContig(),lhp.getFirst().getStart(),lhp.getFirst().getStop(),
+                    qual,prob,rank,lhp.getSecond());
         }
     }