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Bring optimised Jaccard code into main - #72
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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #72 +/- ##
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- Coverage 90.65% 90.32% -0.34%
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Files 17 17
Lines 3232 3359 +127
==========================================
+ Hits 2930 3034 +104
- Misses 302 325 +23 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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johnlees
commented
May 18, 2026
Comment on lines
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+2
| 14412_3#82.contigs_velvet.fa.gz 14412_3#84.contigs_velvet.fa.gz 0.011049058 0.17300157 | ||
| 14412_3#84.contigs_velvet.fa.gz 14412_3#82.contigs_velvet.fa.gz 0.011049058 0.17300157 |
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Getting ~2/3% diff in underlying Jaccard
old: 0.3221537, 0.34842753, 0.37201434, 0.3902269
new: 0.31687897, 0.3392715, 0.3803742, 0.39818868
Which is amplified by regression
Likely a resolution change as wider bins, different hashes
| 14412_3#84.contigs_velvet.fa.gz 5 10 0 0 | ||
| TIGR4.fa.gz 0 0 7 10 | ||
| 14412_3#82.contigs_velvet.fa.gz 10 6 0 0 | ||
| R6.fa.gz 0 0 10 9 |
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For a larger sketch size:
14412_3#82.contigs_velvet.fa.gz 10000 6599 3 3
R6.fa.gz 3 2 10000 6813
14412_3#84.contigs_velvet.fa.gz 6599 10000 2 2
TIGR4.fa.gz 3 2 6813 10000
I think this is just quite noisy at s=10 (and as MOD_SIGN changed, effectively using different hashes)
johnlees
marked this pull request as draft
June 17, 2026 13:26
bbits from 14 -> 16 prevents backwards compatibility
johnlees
marked this pull request as ready for review
July 27, 2026 14:38
Merged
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Closes #68