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DRAFT: SortFastq #38

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kockan wants to merge 1 commit into fulcrumgenomics:main from kockan:can_sort_fastq

kockan commented Aug 21, 2023

Initial attempt at #3
Tested on an empty FASTQ as well as a ~10GB one. It seems to be working.

max-records	fgbio	fqtk
500000	186.07s user 19.88s system 130% cpu 2:37.46 total	221.10s user 27.20s system 82% cpu 4:59.44 total
1000000	194.21s user 21.99s system 114% cpu 3:08.19 total	226.42s user 26.46s system 84% cpu 4:57.96 total
2000000	196.37s user 13.59s system 170% cpu 2:02.82 total	228.77s user 24.76s system 89% cpu 4:44.37 total
4000000	212.98s user 13.57s system 202% cpu 1:52.13 total	230.88s user 20.35s system 119% cpu 3:29.84 total

Looks like fgbio is consistently faster. Should look into why. Library/sorting algorithm/my usage?

Should add unit tests at minimum + any feedback if dev interest in merging.


          Initial code for sort-fastq

713cd16

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