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Hypermutation Handling in PCGR #9

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Merged
merged 38 commits into from
Aug 29, 2025
Merged

Hypermutation Handling in PCGR #9

merged 38 commits into from
Aug 29, 2025

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@qclayssen
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@qclayssen qclayssen commented Aug 19, 2025 •
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Addresses PCGR's limitation in processing hypermutated samples with over 500,000 variants. The current threshold requires filtering, which introduces can discrepancies.

Key Changes:

  1. Chunked VCF Processing:

    • Removed variant downsampling.
    • Split input VCF files into chunks of 450,000 variants.
    • Process chunks in parallel to bypass the variant limit and retain data integrity.

  2. Parallel Processing:

    • Improved efficiency and reduced runtime through parallel chunk processing.

  3. Logging Enhancements:

    • Enhanced logging for better monitoring and error tracking.

qclayssen added 30 commits August 19, 2025 10:06
@qclayssen
add chunk division, parallelization, mergin (spaghetti code)
12b2c1c
@qclayssen
fix path merge vcf and annotation
de5c7f0
@qclayssen
linting organisation
7d4baa2
@qclayssen
linting organisation
d5344e3
@qclayssen
linting
753d70e
@qclayssen
add pathlib and commande excution where need, change commande excution
0b85f98
@qclayssen
add pathlib and commande excution where need, change commande excution
49a7b21
@qclayssen
add back utf-8 encoding
4a06ddc
@qclayssen
add vcf comparator
307c6cf
@qclayssen
Add better thread handling and linting
576c1b3
@qclayssen
change output comparator
a93ece3
@qclayssen
fix overlapping position chunk, variable order
be87fff
@qclayssen
fix library used
bf7508e
@qclayssen
fix import
ec435ba
@qclayssen
improved vcf comparator
6c67a69
@qclayssen
remove filter
2605622
@qclayssen
fix vcf comaprator
801e09c
@qclayssen
add logging
d048dad
@qclayssen
add better login
138316a
@qclayssen
add back MAX_SOMATIC_VARIANTS as threshold
9fdd47c
@qclayssen
change vcf chunk output directory
2a3ac0d
@qclayssen
Fix dir chunks
d0c6600
@qclayssen
reorganise fonctions
4e80143
@qclayssen
linting
5a21516
@qclayssen
simplier logging that was causing problems
5c70195
@qclayssen
keep loging
a0126d7
@qclayssen
more logs
be3ac68
@qclayssen
fix loging path and redundancy
8abbe7c
@qclayssen
work adds loggins
8909952
@qclayssen
fix output dir
e884baf
@qclayssen qclayssen force-pushed the feature/hypermutation branch from 367015f to 7386015 Compare August 26, 2025 05:48
@qclayssen qclayssen self-assigned this Aug 26, 2025
@qclayssen qclayssen added the enhancement New feature or request label Aug 26, 2025
@qclayssen qclayssen requested a review from scwatts August 26, 2025 06:08
@qclayssen qclayssen marked this pull request as ready for review August 26, 2025 06:12
scwatts
scwatts reviewed Aug 28, 2025
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scwatts
scwatts reviewed Aug 28, 2025
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scwatts
scwatts reviewed Aug 29, 2025
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bolt/common/constants.py
## Variation selection (annotation) ##
######################################
MAX_SOMATIC_VARIANTS = 500_000
MAX_SOMATIC_VARIANTS = 450_000
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Update PR description to match this new change

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scwatts commented Aug 29, 2025

I've pushed a small commit to get the tests working again - please take a look and see whether this aligns with your expectations wrt your changes in the PR

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scwatts commented Aug 29, 2025

Approved, please merge at your discretion!

@qclayssen qclayssen mentioned this pull request Oct 28, 2024
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@qclayssen qclayssen merged commit d792557 into release/0.3.0 Aug 29, 2025
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qclayssen added a commit that referenced this pull request Sep 15, 2025
@qclayssen
Hypermutation Handling in PCGR (#9)
5d2c80e
qclayssen added a commit that referenced this pull request Oct 2, 2025
@qclayssen
Hypermutation Handling in PCGR (#9)
f33c48c
qclayssen added a commit that referenced this pull request Oct 2, 2025
@qclayssen
Hypermutation Handling in PCGR (#9)
8780e2f
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@scwatts scwatts scwatts approved these changes

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