From 37c30549f7409c73057e753f35f0236f23d34622 Mon Sep 17 00:00:00 2001
From: David Jones <drj@sanger.ac.uk>
Date: Sat, 8 Sep 2018 17:52:45 +0100
Subject: [PATCH 1/2] Bump version and CHANGES.md

---
 CHANGES.md | 5 +++++
 Makefile   | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/CHANGES.md b/CHANGES.md
index b1a4bc9..f7b31ee 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,5 +1,10 @@
 # CHANGES
 
+## 1.13.4
+
+* Fix incorrect file path introduced in 1.13.3
+* Fixes #82
+
 ## 1.13.3
 
 * Add gzbuffer call after gzopen to ensure we don't hit the limit where many contigs are printed
diff --git a/Makefile b/Makefile
index f0f6272..48a6f7f 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-CAVEMAN_VERSION=1.13.3
+CAVEMAN_VERSION=1.13.4
 TEST_REF?=""
 #Compiler
 CC?=gcc

From 0cc5e01ed88130b4a40bb44cd9a4e34c3e6fe1cc Mon Sep 17 00:00:00 2001
From: David Jones <drj@sanger.ac.uk>
Date: Sat, 8 Sep 2018 17:55:08 +0100
Subject: [PATCH 2/2] Fixes #82 . Correct wrong filename passed

---
 src/estep.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/estep.c b/src/estep.c
index ae997f8..63ca8e3 100644
--- a/src/estep.c
+++ b/src/estep.c
@@ -515,7 +515,7 @@ int estep_main(int argc, char *argv[]){
 	//Open files for output
     uint32_t no_contigs = 0;
     uint32_t total_contigs_length = 0;
-    int res_contig_cnt = fai_access_get_count_length_all_contigs(fa_file, &no_contigs, &total_contigs_length);
+    int res_contig_cnt = fai_access_get_count_length_all_contigs(ref_idx, &no_contigs, &total_contigs_length);
     check(res_contig_cnt==0, "Error establishing contig count and name length.");
 
     uint64_t buf_sz = (no_contigs * (strlen(contig_str) + strlen(assembly) + strlen(species) + 20 )) + total_contigs_length;