bacpop / ska.rust

Split k-mer analysis – version 2
https://docs.rs/ska/latest/ska/
Apache License 2.0
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Add middle base to read count filtering #10

Closed johnlees closed 1 year ago

johnlees commented 1 year ago

Previously the middle base was not considered in filtering minimum counts from reads, now it is. e.g. AAAC T GGTC x30 AAAC A GGTC x1 would previously have appeared in the alignment as W (A or T), but now appears as T. I've added a simple test on this too.

codecov[bot] commented 1 year ago

Codecov Report

Base: 82.77% // Head: 82.78% // Increases project coverage by +0.01% :tada:

Coverage data is based on head (c8cc916) compared to base (e75b0af). Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #10 +/- ## ========================================== + Coverage 82.77% 82.78% +0.01% ========================================== Files 13 13 Lines 1341 1342 +1 Branches 210 210 ========================================== + Hits 1110 1111 +1 Misses 126 126 Partials 105 105 ``` | [Impacted Files](https://codecov.io/gh/bacpop/ska.rust/pull/10?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bacpop) | Coverage Δ | | |---|---|---| | [src/ska\_dict.rs](https://codecov.io/gh/bacpop/ska.rust/pull/10?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bacpop#diff-c3JjL3NrYV9kaWN0LnJz) | `81.42% <100.00%> (ø)` | | | [src/ska\_dict/count\_min\_filter.rs](https://codecov.io/gh/bacpop/ska.rust/pull/10?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bacpop#diff-c3JjL3NrYV9kaWN0L2NvdW50X21pbl9maWx0ZXIucnM=) | `70.73% <100.00%> (+0.73%)` | :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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