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feat: parallelize PGEN reading #273

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feat: parallelize PGEN reading #273

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@aryarm aryarm commented Mar 2, 2025 •
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resolves #253

I've been working on this in my off-time while traveling. (Unlike my other work, this doesn't require access to the internet!) But there's still much to do and this isn't a priority, so this will probably remain unmerged for a while. See #253 for the full TODO list

aryarm added 30 commits September 7, 2024 03:01
@aryarm
refactor: move pgen chunk reading into a separate helper function
8fada1d
@aryarm
recover args from pickling
36482fc
@aryarm
declare shared vars as global instead
3ef62da
@aryarm
enable multiprocessing in GenotypesPLINK.read
a03d9f2
@aryarm
improve explanation for _init_mp
5d6336f
@aryarm
try to optimize cpu usage and use more accurate measure of num CPUs
bc4bb6f
@aryarm
refrain from doing unnecessary benchmarks and remove chunk_size param
c83c905
@aryarm
fix polyfit bug when vals for file type are not generated
777e96a
@aryarm
recover broken plotting of variants
a06cb6b
@aryarm
use ceil instead of floor in chunking
985e6e1
@aryarm
fix chunking bug in bench gts
c880c96
@aryarm
improve splitting of variants across CPUs using Navid's strategy
2a1471d
@aryarm
try to use mp.starmap's chunking
4b1f889
@aryarm
try bigger chunks in bench_gts
413c645
@aryarm
refactor: move pgen chunk reading into a separate helper function
02ea8f0
@aryarm
recover args from pickling
91297da
@aryarm
declare shared vars as global instead
523a5cb
@aryarm
enable multiprocessing in GenotypesPLINK.read
b224d21
@aryarm
improve explanation for _init_mp
0f9b7f4
@aryarm
try to optimize cpu usage and use more accurate measure of num CPUs
f8250d4
@aryarm
refrain from doing unnecessary benchmarks and remove chunk_size param
d0fe09d
@aryarm
fix polyfit bug when vals for file type are not generated
5cb9a05
@aryarm
recover broken plotting of variants
d656dd2
@aryarm
use ceil instead of floor in chunking
3087b08
@aryarm
fix chunking bug in bench gts
e6d8432
@aryarm
improve splitting of variants across CPUs using Navid's strategy
cbfd560
@aryarm
try to use mp.starmap's chunking
424786d
@aryarm
try bigger chunks in bench_gts
5422934
@aryarm
try to load num variants from cyvcf2
2fccf5e
@aryarm
try to add pgen file for example.vcf.gz
eb88bef
@aryarm aryarm marked this pull request as draft March 2, 2025 17:40
@aryarm aryarm mentioned this pull request Mar 20, 2025
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parallelize reading from a PGEN file

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@aryarm