From 478425b3d83911d044c0df123350b43510621565 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 17 Mar 2009 15:37:02 +0000
Subject: [PATCH] Better error messages

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@79 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../src/org/broadinstitute/sting/gatk/TraversalEngine.java     | 2 +-
 .../broadinstitute/sting/gatk/iterators/ReferenceIterator.java | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/playground/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java b/playground/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
index 2644524cd..df54ce815 100755
--- a/playground/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
+++ b/playground/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
@@ -114,7 +114,7 @@ public class TraversalEngine {
     public void setDebugging( final boolean d ) { DEBUGGING = d; }
     public void setSafetyChecking( final boolean beSafeP ) {
         if ( ! beSafeP )
-            System.out.printf("*** Turning off safety checking, I hope you know what you are doing...%n");
+            System.out.printf("*** Turning off safety checking, I hope you know what you are doing.  Errors will result in debugging assert failures and other inscrutable messages...%n");
         this.beSafeP = beSafeP;
     }
 
diff --git a/playground/java/src/org/broadinstitute/sting/gatk/iterators/ReferenceIterator.java b/playground/java/src/org/broadinstitute/sting/gatk/iterators/ReferenceIterator.java
index f4d3038b2..7f7909543 100755
--- a/playground/java/src/org/broadinstitute/sting/gatk/iterators/ReferenceIterator.java
+++ b/playground/java/src/org/broadinstitute/sting/gatk/iterators/ReferenceIterator.java
@@ -116,7 +116,8 @@ public class ReferenceIterator implements Iterator<ReferenceIterator> {
             // we're somewhere on this contig
             if ( seekOffset < offset || seekOffset >= currentContig.length() ) {
                 // bad boy -- can't go backward safely or just beyond the contig length
-                throw new IllegalArgumentException("Bad seek to " + seekOffset + " current: " + offset);
+                throw new IllegalArgumentException(String.format("Invalid seek to %s from %s, which is usually due to out of order reads%n",
+                        new GenomeLoc(currentContig.getName(), seekOffset), new GenomeLoc(currentContig.getName(), offset)));
                 //return null;
             }
             else {