From 2b797ddab348b5a82dde7daecd601f777a37980d Mon Sep 17 00:00:00 2001
From: Keiran Raine <kr2@sanger.ac.uk>
Date: Wed, 20 Mar 2019 15:16:22 +0000
Subject: [PATCH 1/3] Fix index issue on list of protocols to check

---
 Makefile    | 2 +-
 src/estep.c | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/Makefile b/Makefile
index d4b34e2..b40091c 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-CAVEMAN_VERSION=1.13.13
+CAVEMAN_VERSION=1.13.14
 
 TEST_REF?=""
 #Compiler
diff --git a/src/estep.c b/src/estep.c
index 8832bb5..317ce52 100644
--- a/src/estep.c
+++ b/src/estep.c
@@ -91,7 +91,7 @@ static char *tum_prot = "WGS";
 static int max_copy_number = 10;
 static uint32_t default_zbuffer = 1024*1024;
 static char *contig_str = "##contig=<ID=,length=,assembly=,species=>\n";
-char *valid_protocols[3] = {"WGS","WXS","RNA","RNA-Seq","AMPLICON","TARGETED"};
+char *valid_protocols[6] = {"WGS","WXS","RNA","RNA-Seq","AMPLICON","TARGETED"};
 
 void estep_print_usage (int exit_code){
 	printf ("Usage: caveman estep -i jobindex [-f file] [-m int] [-k float] [-b float] [-p float] [-q float] [-x int] [-y int] [-c float] [-d float] [-a int]\n\n");
@@ -323,7 +323,7 @@ int estep_setup_options(int argc, char *argv[]){
 	 int i=0;
 	 int norm_prot_check=0;
 	 int tum_prot_check=0;
-	 for(i=0;i<3;i++){
+	 for(i=0;i<6;i++){
 		if(strcmp(norm_prot,valid_protocols[i])==0){
 			norm_prot_check=1;
 		}

From 6a549940e9af161a10b3112b6b19cd6d318506c6 Mon Sep 17 00:00:00 2001
From: Keiran Raine <kr2@sanger.ac.uk>
Date: Wed, 20 Mar 2019 15:20:21 +0000
Subject: [PATCH 2/3] Fix up error message

---
 src/estep.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/estep.c b/src/estep.c
index 317ce52..34117db 100644
--- a/src/estep.c
+++ b/src/estep.c
@@ -333,12 +333,12 @@ int estep_setup_options(int argc, char *argv[]){
 	 }
 
    if(norm_prot_check==0){
-		printf("Normal protocol '%s' is invalid should be one of (WGS|WXS|RNA).",norm_prot);
+		printf("Normal protocol '%s' is invalid should be one of (WGS|RNA|RNA-Seq|AMPLICON|TARGETED).\n",norm_prot);
 		estep_print_usage(1);
    }
 
    if(tum_prot_check==0){
-		printf("Tumour protocol '%s' is invalid should be one of (WGS|WXS|RNA).",tum_prot);
+		printf("Tumour protocol '%s' is invalid should be one of (WGS|RNA|RNA-Seq|AMPLICON|TARGETED).\n",tum_prot);
 		estep_print_usage(1);
    }
 

From 106ba8ea6d8032ac030ffaa4b36d570bd5f3d677 Mon Sep 17 00:00:00 2001
From: Keiran Raine <kr2@sanger.ac.uk>
Date: Wed, 20 Mar 2019 15:21:58 +0000
Subject: [PATCH 3/3] Detail changes

---
 CHANGES.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGES.md b/CHANGES.md
index 49ffef0..05fcd01 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,5 +1,9 @@
 # CHANGES
 
+## 1.13.14
+
+* Fix array length index, check loop length and error messages related to 1.13.13.
+
 ## 1.13.13
 
 * Add AMPLICON and TARGETED to accepted protocol list. Change RNA-seq, but also keep RNA.