From 6281c1db6f2545b7f33f33d930cbb2cd741d0ca6 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 18 Mar 2011 02:58:29 +0000
Subject: [PATCH] A nicer error (UserException now) for malformed genome locs

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5465 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/utils/GenomeLocParser.java    | 6 +++---
 .../sting/utils/exceptions/UserException.java              | 7 +++++++
 2 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
index 8cc405a21..670b90d43 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
@@ -448,11 +448,11 @@ public class GenomeLocParser {
     private void exceptionOnInvalidGenomeLocBounds(GenomeLoc locus) {
         int contigSize = contigInfo.getSequence(locus.getContigIndex()).getSequenceLength();
         if(locus.getStart() > contigSize)
-            throw new ReviewedStingException(String.format("GenomeLoc is invalid: locus start %d is after the end of contig %s",locus.getStart(),locus.getContig()));
+            throw new UserException.MalformedGenomeLoc("GenomeLoc is invalid: locus start is after the end of contig",locus);
         if(locus.getStop() > contigSize)
-            throw new ReviewedStingException(String.format("GenomeLoc is invalid: locus stop %d is after the end of contig %s",locus.getStop(),locus.getContig()));
+            throw new UserException.MalformedGenomeLoc("GenomeLoc is invalid: locus stop is after the end of contig",locus);
         if (locus.getStart() > locus.getStop()) {
-            throw new ReviewedStingException("Parameters to GenomeLocParser are incorrect: the start position is greater than the end position");
+            throw new UserException.MalformedGenomeLoc("Parameters to GenomeLocParser are incorrect: the start position is greater than the end position", locus);
         }
     }
 
diff --git a/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
index 41499af1c..62fca6524 100755
--- a/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
+++ b/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
@@ -30,6 +30,7 @@ import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.GenomeLoc;
 
 import java.io.File;
 import java.util.Arrays;
@@ -54,6 +55,12 @@ public class UserException extends ReviewedStingException {
         }
     }
 
+    public static class MalformedGenomeLoc extends UserException {
+        public MalformedGenomeLoc(String message, GenomeLoc loc) {
+            super(String.format("Badly formed genome loc: %s: %s", message, loc));
+        }
+    }
+
     public static class BadInput extends UserException {
         public BadInput(String message) {
             super(String.format("Bad input: %s", message));