From f87bae169276ccb7e78600ec46f2fa2b78f8dec2 Mon Sep 17 00:00:00 2001
From: leggettr <richard.leggett@tgac.ac.uk>
Date: Fri, 7 Feb 2014 10:31:35 +0000
Subject: [PATCH] Reinstated missing -e option

---
 src/nextclip.c | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/nextclip.c b/src/nextclip.c
index 199dc20..68da4fb 100755
--- a/src/nextclip.c
+++ b/src/nextclip.c
@@ -140,8 +140,8 @@ typedef struct {
 /*----------------------------------------------------------------------*
  * Globals
  *----------------------------------------------------------------------*/
-char single_junction_adaptor[] = "CTGTCTCTTATACACATCT";
-char duplicate_junction_adaptor[] = "CTGTCTCTTATACACATCTAGATGTGTATAAGAGACAG";
+char single_junction_adaptor[128] = "CTGTCTCTTATACACATCT";
+char duplicate_junction_adaptor[128] = "CTGTCTCTTATACACATCTAGATGTGTATAAGAGACAG";
 char* external_adaptors[2] = {"GATCGGAAGAGCACACGTCTGAACTCCAGTCAC", "GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"};
 int minimum_read_size = 25;
 int strict_double_match = 34;
@@ -419,6 +419,9 @@ void parse_command_line(int argc, char* argv[], MPStats* stats)
             case 'd':
                 remove_duplicates=1;
                 break;
+            case 'e':
+                use_category_e = 1;
+                break;
             case 'h':
                 usage();
                 exit(0);