mod to display cmdline options to sam header #260
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marcelm
reviewed
Apr 3, 2023
src/main.cpp
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| @@ -131,6 +131,11 @@ void show_progress_until_done(std::vector<int>& worker_done, std::vector<Alignme | |||
| int run_strobealign(int argc, char **argv) { | |||
| auto opt = parse_command_line_arguments(argc, argv); | |||
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| std::stringstream cmd_line; | |||
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Can you move this into the if (map_param.is_sam_out) { block below? Then it’s closer to where it’s used.
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Thanks for your comment. You are indeed correct. I will fix it.
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I fixed it. Would you check it please.
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Thanks again! We may need to add an option to disable adding the |
rebjannik
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May 17, 2025
mod to display cmdline options to sam header
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Hi.
I am in the process of evaluating strobealign. I think it is very nice software.
By the way, the @pg tag in the SAM header, the spec says that the CL tag should show the command line options when run the analysis.
So I thought it was correct to modify it this way.
I would be happy if you could merge them.