From 86871bd1e36534eabdac8ff5e3dc371aaad3fef4 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Wed, 26 Oct 2011 15:56:41 -0400
Subject: [PATCH] Throw a UserException in the BQSR when there is no data
 instead of creating an empty csv file

---
 .../gatk/walkers/recalibration/CountCovariatesWalker.java      | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
index 1bdb70bdd..88a9668cc 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
@@ -526,6 +526,9 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
      */
     public void onTraversalDone( CountedData sum ) {
         logger.info( "Writing raw recalibration data..." );
+        if( sum.countedBases == 0L ) {
+            throw new UserException.BadInput("Could not find any usable data in the input BAM file(s).");
+        }
         outputToCSV( sum, RECAL_FILE );
         logger.info( "...done!" );
     }