From 637e0cf1512c68e8964b3e1d5bce6d0755cad61b Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Thu, 11 Oct 2012 13:59:21 -0400
Subject: [PATCH] CountReads does not permit the use of output files

---
 .../src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java | 1 -
 1 file changed, 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java
index 301fa5b9b..1d2c6c9cc 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java
@@ -33,7 +33,6 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
  * java -Xmx2g -jar GenomeAnalysisTK.jar \
  *   -R ref.fasta \
  *   -T CountReads \
- *   -o output.txt \
  *   -I input.bam \
  *   [-L input.intervals]
  * </pre>