From 1092dd6e254e601d15df0ffdb1dc122d4e1da8ac Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 19 Jun 2014 10:05:51 -0400
Subject: [PATCH] From Carlos Barroto: switch outputRoot in SplitSamFile to an
 empty string instead of null.

---
 .../gatk/tools/walkers/readutils/SplitSamFile.java              | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java
index b19a2d735..157a44f0a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java
@@ -57,7 +57,7 @@ import java.util.Map;
 @Requires({DataSource.READS})
 public class SplitSamFile extends ReadWalker<SAMRecord, Map<String, SAMFileWriter>> {
     @Argument(fullName="outputRoot", doc="output BAM file", required=false)
-    public String outputRoot = null;
+    public String outputRoot = "";
 
     @Argument(fullName = "bam_compression", shortName = "compress", doc = "Compression level to use for writing BAM files", required = false)
     public Integer BAMcompression = 5;