Use stored alignments if available

chanzuckerberg / shasta

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

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Use stored alignments if available #110

Closed bagashe closed 4 years ago

bagashe commented 4 years ago

Here's the speed up (time saved) for different options. 15.5% time saved across the board and about 18-20% improvement in compute speed.

714s -> 600s. (disk/ssd, filesystem) 633s -> 533s (memory 4k pages, anonymous) 629s -> 533s (memory 2m pages, anonymous) 629s -> 524s (memory 2m pages, filesystem)

333s -> 282s (memory 2m pages, filesystem, alignMethodFor*Graph 3)

paoloczi commented 4 years ago

The comments I made are cosmetic and optional, so I am merging the PR as is. You may want to consider making those changes at a later time.

bagashe commented 4 years ago

Cool. I will make those changes some time today. Excited about a full assembly. Yay!