From 308e5b6cf13878927c017b8b5cd1836fb694f984 Mon Sep 17 00:00:00 2001
From: Bo Li <bli25@berkeley.edu>
Date: Tue, 10 Nov 2015 20:58:24 -0800
Subject: [PATCH] Fixed a small bug in rsem-prepare-reference

---
 rsem-prepare-reference | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/rsem-prepare-reference b/rsem-prepare-reference
index ab0ebce..4ac982c 100755
--- a/rsem-prepare-reference
+++ b/rsem-prepare-reference
@@ -104,7 +104,8 @@ else {
     &runCommand($command);
 }
 
-$command = "rsem-preref $ARGV[1].transcripts.fa $polyAChoice $ARGV[1] -l $polyALen";
+$command = "rsem-preref $ARGV[1].transcripts.fa $polyAChoice $ARGV[1]";
+if ($polyAChoice != 1) { $command .= " -l $polyALen"; }
 if ($polyAChoice == 2) { $command .= " -f $subsetFile"; }
 if ($quiet) { $command .= " -q"; }