From b4a2112a0dfa5c33cc4bf2814cd15364fe50e961 Mon Sep 17 00:00:00 2001
From: fromer <fromer@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 13 Jan 2011 17:19:20 +0000
Subject: [PATCH] Added the "previous locus" to interesting sites VCF (locus
 with respect to which the site is phased)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4990 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../varianteval/GenotypePhasingEvaluator.java     | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java
index e5b55bf6f..24e10bb81 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java
@@ -141,7 +141,8 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
                     samplePrevGenotypes.put(samp, curLocus, compSampGt, evalSampGt);
 
                     if (prevCompAndEval != null) {
-                        logger.debug("Potentially phaseable het locus: " + curLocus + " [relative to previous het locus: " + prevCompAndEval.getLocus() + "]");
+                        GenomeLoc prevLocus = prevCompAndEval.getLocus();
+                        logger.debug("Potentially phaseable het locus: " + curLocus + " [relative to previous het locus: " + prevLocus + "]");
                         PhaseStats ps = samplePhasingStatistics.ensureSampleStats(samp);
 
                         boolean compSampIsPhased = genotypesArePhasedAboveThreshold(compSampGt);
@@ -149,11 +150,11 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
                         if (compSampIsPhased || evalSampIsPhased) {
                             if (!evalSampIsPhased) {
                                 ps.onlyCompPhased++;
-                                interesting.addReason("ONLY_COMP", samp, group, "");
+                                interesting.addReason("ONLY_COMP", samp, group, prevLocus, "");
                             }
                             else if (!compSampIsPhased) {
                                 ps.onlyEvalPhased++;
-                                interesting.addReason("ONLY_EVAL", samp, group, "");
+                                interesting.addReason("ONLY_EVAL", samp, group, prevLocus, "");
                             }
                             else { // both comp and eval are phased:                        
                                 AllelePair prevCompAllelePair = new AllelePair(prevCompAndEval.getCompGenotpye());
@@ -169,12 +170,12 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
                                     Double compPQ = getPQ(compSampGt);
                                     Double evalPQ = getPQ(evalSampGt);
                                     if (compPQ != null && evalPQ != null && MathUtils.compareDoubles(compPQ, evalPQ) != 0)
-                                        interesting.addReason("PQ_CHANGE", samp, group, compPQ + " -> " + evalPQ);
+                                        interesting.addReason("PQ_CHANGE", samp, group, prevLocus, compPQ + " -> " + evalPQ);
                                 }
                                 else {
                                     ps.phasesDisagree++;
                                     logger.debug("SWITCHED locus: " + curLocus);
-                                    interesting.addReason("SWITCH", samp, group, toString(prevCompAllelePair, compAllelePair) + " -> " + toString(prevEvalAllelePair, evalAllelePair));
+                                    interesting.addReason("SWITCH", samp, group, prevLocus, toString(prevCompAllelePair, compAllelePair) + " -> " + toString(prevEvalAllelePair, evalAllelePair));
                                 }
                             }
                         }
@@ -243,8 +244,8 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
             sb = new StringBuilder();
         }
 
-        public void addReason(String category, String sample, VariantEvalWalker.EvaluationContext evalGroup, String reason) {
-             sb.append(category + "(" + sample + " [" + evalGroup.compTrackName + ", " + evalGroup.evalTrackName + "]): " + reason + ";");
+        public void addReason(String category, String sample, VariantEvalWalker.EvaluationContext evalGroup, GenomeLoc prevLoc, String reason) {
+             sb.append(category + "(" + sample + ", previous= " + prevLoc + " [" + evalGroup.compTrackName + ", " + evalGroup.evalTrackName + "]): " + reason + ";");
         }
 
         public String toString() {