From c209ba55aa8fe33b49cd8b5501da4559632b2331 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 5 Jan 2010 13:55:20 +0000
Subject: [PATCH] More informative error message

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2499 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/genotyper/EmpiricalSubstitutionProbabilities.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EmpiricalSubstitutionProbabilities.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EmpiricalSubstitutionProbabilities.java
index 4045e2ed4..04107ddb3 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EmpiricalSubstitutionProbabilities.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EmpiricalSubstitutionProbabilities.java
@@ -229,7 +229,7 @@ public class EmpiricalSubstitutionProbabilities extends FourBaseProbabilities {
 
         if ( pl == SequencerPlatform.UNKNOWN ) {
             if ( raiseErrorOnUnknownPlatform )
-                throw new RuntimeException("Unknown Sequencer platform for read " + read.format());
+                throw new RuntimeException("Unknown Sequencer platform for read " + read.format() + "; your BAM file is missing the PL tag for some read groups.  Please specify a default platform.  See your walker's documentation to accomplish this");
             else {
                 pl = defaultPlatform;
                 //System.out.printf("Using default platform %s", pl);
@@ -249,4 +249,4 @@ public class EmpiricalSubstitutionProbabilities extends FourBaseProbabilities {
 
         return log10p;
     }
-}
\ No newline at end of file
+}