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Correct estep.c help docs. WGX -> WXS. Fixes #61 #73

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Mar 6, 2018
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Correct estep.c help docs. WGX -> WXS. Fixes #61 #73

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4 changes: 2 additions & 2 deletions src/estep.c
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Original file line number Diff line number Diff line change
Expand Up @@ -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);
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