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chasewnelson / SNPGenie

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
GNU General Public License v3.0
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Ignore genes that are not multiples of 3 #32

Open jckhearn opened 4 years ago

jckhearn commented 4 years ago

Hello Chase,

I'm using SNPGenie on some genome-wide pooled sequencing. SNPGenie stops at the start when it finds loci in the gtf that are not multiples of 3. Is it possible for a SNPGenie option to ignore these loci (with a note in the log) and carry on with an analysis?

This would speed up batch-processing considerably and not affect downstream analyses in my case.

Best wishes, Jack

singing-scientist commented 4 years ago

Dear Jack:

Thanks very much for using SNPGenie and for the good suggestion. Unfortunately, I am too swamped at the moment to make the improvement you recommend, but I will leave this issue open with the hope to get to it soon. In the meantime, I feel it best to leave as-is, as modifying SNPGenie to carry on with analysis could lead to unintended bugs, or else erroneous results in the case of new users. Please do let me know if you have any other suggestions.

With gratitude, Chase

jckhearn commented 4 years ago

Okay thanks!