tskit-dev / tsinfer

Infer a tree sequence from genetic variation data.
GNU General Public License v3.0
56 stars 13 forks source link

Variant data #956

Closed hyanwong closed 2 months ago

hyanwong commented 2 months ago

Add example of excluding chromosomes using site masks, and change zarr.load() to the more recommended zarr.open().

We have had some users try to infer with VCFs containing multiple chromosomes, so the examples here are useful.

codecov[bot] commented 2 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 93.23%. Comparing base (1c355ae) to head (962b7eb). Report is 1 commits behind head on main.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #956 +/- ## ======================================= Coverage 93.23% 93.23% ======================================= Files 18 18 Lines 6299 6299 Branches 1139 1139 ======================================= Hits 5873 5873 Misses 290 290 Partials 136 136 ``` | [Flag](https://app.codecov.io/gh/tskit-dev/tsinfer/pull/956/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | Coverage Δ | | |---|---|---| | [C](https://app.codecov.io/gh/tskit-dev/tsinfer/pull/956/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | `93.23% <ø> (ø)` | | | [python](https://app.codecov.io/gh/tskit-dev/tsinfer/pull/956/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | `95.65% <ø> (ø)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev#carryforward-flags-in-the-pull-request-comment) to find out more.

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.