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bacpop / ska.rust

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

Add k-mer counts per sample to ska nk; efficiency of dup counting #40

Closed johnlees closed 1 year ago

johnlees commented 1 year ago

ska nk now looks like:

ska_version=0.2.2
k=21
k_bits=64
rc=true
k-mers=3228084
samples=28
sample_names=["19183_4#73", "12673_8#29", "12673_8#31", "12754_5#61", "12754_5#89", "12754_5#47", "12754_5#32", "12754_5#78", "12754_4#85", "12754_5#74", "19183_4#57", "12754_5#36", "19183_4#49", "19183_4#79", "19183_4#60", "12754_5#24", "12754_5#22", "12754_5#71", "12673_8#26", "12754_5#95", "12754_5#86", "12673_8#24", "19183_4#61", "12673_8#41", "12754_4#66", "12754_5#80", "12754_5#84", "19183_4#78"]
sample_kmers=[2872587, 2997448, 2949719, 2997496, 2997178, 2912749, 2996491, 2997221, 2949102, 2997454, 2914109, 2912237, 2872518, 2869957, 2872470, 2997992, 2997647, 2958512, 2998099, 2997290, 2950253, 3027707, 2997881, 2907920, 2911447, 2997644, 2944830, 2915080]

Also small change to how duplicates are counted which doesn't change any results but tidies the code a bit

Closes #39

codecov[bot] commented 1 year ago

Codecov Report

Patch coverage: 100.00% and project coverage change: -0.03 :warning:

Comparison is base (62b752c) 92.66% compared to head (d54ac01) 92.64%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #40 +/- ## ========================================== - Coverage 92.66% 92.64% -0.03% ========================================== Files 16 16 Lines 2140 2147 +7 ========================================== + Hits 1983 1989 +6 - Misses 157 158 +1 ``` | [Impacted Files](https://app.codecov.io/gh/bacpop/ska.rust/pull/40?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://app.codecov.io/gh/bacpop/ska.rust/pull/40?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bacpop#diff-c3JjL2xpYi5ycw==) | `82.07% <ø> (-0.20%)` | :arrow_down: | | [src/merge\_ska\_array.rs](https://app.codecov.io/gh/bacpop/ska.rust/pull/40?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bacpop#diff-c3JjL21lcmdlX3NrYV9hcnJheS5ycw==) | `98.81% <100.00%> (+0.02%)` | :arrow_up: | | [src/ska\_ref.rs](https://app.codecov.io/gh/bacpop/ska.rust/pull/40?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bacpop#diff-c3JjL3NrYV9yZWYucnM=) | `96.20% <100.00%> (ø)` | |

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