Merge pull request #73 from cancerit/feature/wgx_options_fix

Correct estep.c help docs. WGX -> WXS. Fixes #61

src/estep.c

@@ -112,8 +112,8 @@ void estep_print_usage (int exit_code){
 	printf("-w  --species [string]                           Species name (eg Human), required if bam header SQ lines do not contain AS and SP information.\n");
 	printf("-n  --normal-copy-number [int]                   Copy number to use when filling gaps in the normal copy number file [default:%d].\n",normal_copy_number);
 	printf("-t  --tumour-copy-number [int]                   Copy number to use when filling gaps in the tumour copy number file [default:%d].\n",tumour_copy_number);
-	printf("-l  --normal-protocol [string]                   Normal protocol. Ideally this should match -r but not checked (WGS|WGX|RNA) [default:%s].\n",norm_prot);
-	printf("-r  --tumour-protocol [string]                   Tumour protocol. Ideally this should match -l but not checked (WGS|WGX|RNA) [default:%s].\n",tum_prot);
+	printf("-l  --normal-protocol [string]                   Normal protocol. Ideally this should match -r but not checked (WGS|WXS|RNA) [default:%s].\n",norm_prot);
+	printf("-r  --tumour-protocol [string]                   Tumour protocol. Ideally this should match -l but not checked (WGS|WXS|RNA) [default:%s].\n",tum_prot);
 	printf("-P  --normal-platform [string]                   Normal platform. Overrides the values retrieved from bam header.\n");
 	printf("-T  --tumour-platform [string]                   Tumour platform. Overrides the values retrieved from bam header.\n");
 	printf("-M  --max-copy-number [int]                      Maximum copy number permitted. If exceeded the copy number for the offending region will be set to this value. [default:%d].\n",max_copy_number);