Backport of fix for #74 as primary has moved on

Makefile

@@ -1,4 +1,4 @@
-CAVEMAN_VERSION=1.11.3
+CAVEMAN_VERSION=1.11.4
 TEST_REF?=""
 #Compiler
 CC?=gcc

src/split.c

@@ -1,5 +1,5 @@
 /**   LICENSE
-* Copyright (c) 2014-2015 Genome Research Ltd.
+* Copyright (c) 2014-2018 Genome Research Ltd.
 *
 * Author: Cancer Genome Project cgpit@sanger.ac.uk
 *
@@ -333,7 +333,9 @@ int split_main(int argc, char *argv[]){
 				//Set old stop position (Min of curr_t_pos & curr_n_pos)
 				sect_stop = min(curr_t_pos,curr_n_pos);
 				//This is the position on which to separate the split sections so print it.
-				split_access_print_section(output,chr_name,sect_start,sect_stop);
+				if(sect_stop>0) {
+					split_access_print_section(output,chr_name,sect_start,sect_stop);
+				}
 				//printf("Found %d reads for %s:%d-%d\n",rd_count,chr_name,sect_start,sect_stop);
 				//Reset read count
 				rd_count=1;//Set as 1 due to the way the loop records read counts .