From dce2e29ade58fad3aba8889589dc747550c28a55 Mon Sep 17 00:00:00 2001
From: Ron Levine <rlevine@broadinstitute.org>
Date: Wed, 18 Jan 2017 15:11:52 -0500
Subject: [PATCH] Change ALLOW_N_CIGARS to ALLOW_N_CIGAR_READS in doc

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

diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java
index 441a01c04..b682e3bfc 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java
@@ -107,7 +107,7 @@ import java.util.ArrayList;
  *   -R reference.fasta \
  *   -I input.bam \
  *   -o output.bam \
- *   -U ALLOW_N_CIGARS
+ *   -U ALLOW_N_CIGAR_READS
  * </pre>
  * 
  * <h3>Note</h3>