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Published 20 hours ago • verified publisher icon andreas-wilm

Optimizations needed: twice as slow as LoFreq2

Open andreas-wilm opened this issue 5 years ago • 3 comments

andreas-wilm avatar Dec 06 '19 06:12 andreas-wilm

Measured against release install of LoFreq3 on first 100k bases of spike-in-viterbi.down10p.bam. Same is true for call -p vs plpsummary

andreas-wilm avatar Dec 06 '19 06:12 andreas-wilm

Needs pileup engine rewrite

andreas-wilm avatar Jul 06 '20 03:07 andreas-wilm

Completed with merging pileup-buffer-tags branch. For specific data-sets old LF3 version was 3x of LF2, after merging it's 2X.

Further optimization idea: use refs in inner loops. See https://forum.nim-lang.org/t/7364

andreas-wilm avatar Jan 15 '21 05:01 andreas-wilm