Multiple scan of the file?

Feb 20, 2012 at 12:36 PM

Hi there,

I noticed that this program is scanning the file multiple times for each of the graph, is there any reason for this or why not only scan the file once? (With large files the waiting is too long.)

Anyway, good work!

Best,

dong

Coordinator
Feb 21, 2012 at 2:17 AM

Hi Dong,

Thanks for your feedback and trying out SeQCoS! Yes you bring up a good point and it is currently a major limitation of the program. It is something I am looking to work on for a future update (e.g. iterate through the file only once). There are a few other areas I think I can optimize in the code (this is my first major project in C#). In my experience, the longest running process is the boxplot by position graph. Although it does this all in memory, it naively has to summarize the quality scores ALL sequences in the file on a position-by-position basis. In the meantime, you can try breaking up your file into smaller parts.

Best,

Kevin

Coordinator
Sep 1, 2012 at 6:48 PM
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