From cff7c6ddceaa7ae4dec9df14bc8377a05af854df Mon Sep 17 00:00:00 2001 From: ebanks Date: Sun, 21 Nov 2010 02:08:11 +0000 Subject: [PATCH] These are user exceptions git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4712 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/annotator/genomicannotator/JoinTable.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java index 1b2c85b3e..c57aacb5b 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java @@ -119,7 +119,7 @@ public class JoinTable while((line = br.readLine()) != null) { final ArrayList columnValues = parser.parseLine(line); if ( columnValues.size() < columnNames.size() ) - throw new IllegalStateException("The file: " + filename + " is malformed as there are not a sufficient number of columns for this line: " + line); + throw new UserException.BadInput("the file: " + filename + " is malformed as there are not a sufficient number of columns for this line: " + line); final String joinColumnValue = columnValues.get(localColumnNameIdx); put(joinColumnValue, columnValues, filename); } @@ -218,9 +218,9 @@ public class JoinTable */ protected void put(String joinColumnValue, ArrayList record, String filename) { if ( joinColumnValueToRecords.containsKey(joinColumnValue) ) - throw new IllegalStateException("The file " + filename + " contains non-unique entries for the requested column, which isn't allowed."); + throw new UserException.BadInput("the file " + filename + " contains non-unique entries for the requested column, which isn't allowed."); joinColumnValueToRecords.put(joinColumnValue, record); if ( joinColumnValueToRecords.size() > maxSize ) - throw new IllegalStateException("The file " + filename + " contains more than the maximum number (" + maxSize + ") of allowed rows (see the --maxJoinTableSize argument)."); + throw new UserException.BadInput("the file " + filename + " contains more than the maximum number (" + maxSize + ") of allowed rows (see the --maxJoinTableSize argument)."); } }