Gaurav
Gaurav
Great suggestion, thanks @rob-p and @gmarcais . Somehow, I missed it. I added it in the latest commit. Speed now from 3 runs: ``` real 1m19.884s 1m15.891s 1m21.462s user 8m9.189s...
Sure. ``` reg[0]: ([ATGC]{9,10})(CAGAGC)([ATGC]{8})([ATGC]{10}) reg[1]: ([ATGC]{1,}) ``` For other custom geometries, these can be obtained by uncommenting lines 1473 and 1474 in `src/AlevinUtils.cpp`.
I can try '^' and '$' after lunch. I didn't test any other library, since boost was already a pre-requisite for salmon and my focus was on getting it to...
Including '^' didn't change the speed, and '$' can't be added as there are extra bases (not in protocol spec) at end which can vary in number. ``` real 1m19.392s...
Hi @rob-p! Thanks for all the great suggestions and comments. I have addressed all of them. I also tested the speed after the changes. The test was done 3 times...
Yes, @rob-p! It's an improvement from ~33% to ~19% slower (I'm not sure why sd is high for custom testing though). Yeah, I'm eager to hear your views too, @gmarcais.
Hello, Thanks for raising and discussing the issue. I am facing the same issue. Could you tell me if this is resolved? Thanks.
Yes, finishing up #734 would be additionally helpful.