bacpop / ska.rust

Split k-mer analysis – version 2
https://docs.rs/ska/latest/ska/
Apache License 2.0
56 stars 4 forks source link

Faster filter for reads #20

Closed johnlees closed 1 year ago

johnlees commented 1 year ago

Uses a hybrid approach of blocked bloom + countmin. Also improved by reducing number of dictionary modifications

codecov[bot] commented 1 year ago

Codecov Report

Base: 82.11% // Head: 82.42% // Increases project coverage by +0.30% :tada:

Coverage data is based on head (f215c90) compared to base (ba5b0d2). Patch coverage: 91.37% of modified lines in pull request are covered.

:exclamation: Current head f215c90 differs from pull request most recent head 8aaca9e. Consider uploading reports for the commit 8aaca9e to get more accurate results

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #20 +/- ## ========================================== + Coverage 82.11% 82.42% +0.30% ========================================== Files 15 15 Lines 1510 1553 +43 Branches 265 272 +7 ========================================== + Hits 1240 1280 +40 - Misses 104 106 +2 - Partials 166 167 +1 ``` | [Impacted Files](https://codecov.io/gh/bacpop/ska.rust/pull/20?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bacpop) | Coverage Δ | | |---|---|---| | [src/lib.rs](https://codecov.io/gh/bacpop/ska.rust/pull/20?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bacpop#diff-c3JjL2xpYi5ycw==) | `72.97% <ø> (+0.09%)` | :arrow_up: | | [src/ska\_dict/bit\_encoding.rs](https://codecov.io/gh/bacpop/ska.rust/pull/20?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bacpop#diff-c3JjL3NrYV9kaWN0L2JpdF9lbmNvZGluZy5ycw==) | `98.96% <ø> (ø)` | | | [src/ska\_dict.rs](https://codecov.io/gh/bacpop/ska.rust/pull/20?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bacpop#diff-c3JjL3NrYV9kaWN0LnJz) | `86.95% <75.00%> (+0.80%)` | :arrow_up: | | [src/ska\_dict/count\_min\_filter.rs](https://codecov.io/gh/bacpop/ska.rust/pull/20?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bacpop#diff-c3JjL3NrYV9kaWN0L2NvdW50X21pbl9maWx0ZXIucnM=) | `83.82% <94.00%> (+10.49%)` | :arrow_up: | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bacpop). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bacpop)

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