From c6351a11d6384b7b0f14f0956f911cb6d5ff4208 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sat, 18 Sep 2010 16:10:42 +0000
Subject: [PATCH] Clearer logger output when not using by-hapmap

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4308 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../variantrecalibration/GenerateVariantClustersWalker.java   | 4 +++-
 .../walkers/variantrecalibration/VariantRecalibrator.java     | 4 +++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
index ccc951540..df737e90f 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
@@ -139,7 +139,9 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
                 logger.info("Found input variant track with name " + d.getName());
             } else if ( d.getName().equals(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME) ) {
                 logger.info("Found dbSNP track for use in training with weight = " + WEIGHT_DBSNP);
-                logger.info("\tsites in dbSNP track tagged with by-hapmap validation status will be used in training with weight = " + WEIGHT_HAPMAP);
+                if( !NO_BY_HAPMAP_VALIDATION_STATUS ) {                                
+                    logger.info("\tsites in dbSNP track tagged with by-hapmap validation status will be used in training with weight = " + WEIGHT_HAPMAP);
+                }
                 foundDBSNP = true;
             } else if ( d.getName().equals("hapmap") ) {
                 logger.info("Found HapMap track for use in training with weight = " + WEIGHT_HAPMAP);
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 0fd7a937c..aafc3054d 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -159,7 +159,9 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
                 logger.info("Found input variant track with name " + d.getName());
             } else if ( d.getName().equals(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME) ) {
                 logger.info("Found dbSNP track with prior probability = Q" + PRIOR_DBSNP);
-                logger.info("\tsites in dbSNP track tagged with by-hapmap validation status will be given prior probability = Q" + PRIOR_HAPMAP);
+                if( !NO_BY_HAPMAP_VALIDATION_STATUS ) {
+                    logger.info("\tsites in dbSNP track tagged with by-hapmap validation status will be given prior probability = Q" + PRIOR_HAPMAP);
+                }
                 foundDBSNP = true;
             } else if ( d.getName().equals("hapmap") ) {
                 logger.info("Found HapMap track with prior probability = Q" + PRIOR_HAPMAP);