Add ska distance, and clustering script

[johnlees]

Adds ska distance. Also includes python script for making clusters and drawing them in Microreact.

TODO:

• [x] Add a test with more than two samples
• [x] Fix mismatches when ambiguous bases are filtered
• [x] Fix ambiguous bases when a frequency filter is used

Closes #26, closes #25

[codecov[bot]]

Codecov Report

Patch coverage: 96.34% and project coverage change: +11.56 :tada:

Comparison is base (899e5fd) 80.90% compared to head (86f3a37) 92.47%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #35 +/- ## =========================================== + Coverage 80.90% 92.47% +11.56% =========================================== Files 16 16 Lines 1922 2086 +164 Branches 355 0 -355 =========================================== + Hits 1555 1929 +374 - Misses 142 157 +15 + Partials 225 0 -225 ``` | [Impacted Files](https://app.codecov.io/gh/bacpop/ska.rust/pull/35?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bacpop) | Coverage Δ | | |---|---|---| | [src/cli.rs](https://app.codecov.io/gh/bacpop/ska.rust/pull/35?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bacpop#diff-c3JjL2NsaS5ycw==) | `74.67% <68.75%> (+7.29%)` | :arrow_up: | | [src/lib.rs](https://app.codecov.io/gh/bacpop/ska.rust/pull/35?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bacpop#diff-c3JjL2xpYi5ycw==) | `81.68% <95.65%> (+13.79%)` | :arrow_up: | | [src/coverage.rs](https://app.codecov.io/gh/bacpop/ska.rust/pull/35?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bacpop#diff-c3JjL2NvdmVyYWdlLnJz) | `97.34% <100.00%> (+17.55%)` | :arrow_up: | | [src/generic\_modes.rs](https://app.codecov.io/gh/bacpop/ska.rust/pull/35?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bacpop#diff-c3JjL2dlbmVyaWNfbW9kZXMucnM=) | `100.00% <100.00%> (+31.34%)` | :arrow_up: | | [src/merge\_ska\_array.rs](https://app.codecov.io/gh/bacpop/ska.rust/pull/35?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bacpop#diff-c3JjL21lcmdlX3NrYV9hcnJheS5ycw==) | `98.79% <100.00%> (+7.88%)` | :arrow_up: | | [src/ska\_dict/bit\_encoding.rs](https://app.codecov.io/gh/bacpop/ska.rust/pull/35?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bacpop#diff-c3JjL3NrYV9kaWN0L2JpdF9lbmNvZGluZy5ycw==) | `100.00% <100.00%> (+1.03%)` | :arrow_up: | ... and [9 files with indirect coverage changes](https://app.codecov.io/gh/bacpop/ska.rust/pull/35/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bacpop)

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