poseidon-framework / poseidon-hs

A toolset to work with modular genotype databases in the Poseidon format
https://poseidon-framework.github.io/#/trident
MIT License
7 stars 2 forks source link

Jannocoalesce minor adjustments #284

Closed nevrome closed 9 months ago

nevrome commented 10 months ago

As suggested:

The rest are cosmetic changes to make code and output more consistent with other parts of trident.

Here's how the output can look now:

$ trident jannocoalesce -s ../../community-archive/2021_CarlhoffNature/2021_CarlhoffNature.janno -t 2021_CarlhoffNature.janno --stripIdRegex "_SG_MNT" --debug
trident v1.4.1.0 for poseidon v2.5.0, v2.6.0, v2.7.0, v2.7.1
https://poseidon-framework.github.io

[Debug]   [2023-12-20 13:13:44] Reading: ../../community-archive/2021_CarlhoffNature/2021_CarlhoffNature.janno
[Debug]   [2023-12-20 13:13:44] 1 samples in this file
[Debug]   [2023-12-20 13:13:44] Reading: 2021_CarlhoffNature.janno
[Debug]   [2023-12-20 13:13:44] 6 samples in this file
[Debug]   [2023-12-20 13:13:44] Additional columns: Eager_ID (?), Main_ID (?), RateErrX (?), RateErrY (?), RateX (?), RateY (?)
[Info]    [2023-12-20 13:13:44] Starting to coalesce...
[Info]    [2023-12-20 13:13:44] matched target GUP001_SG_MNT with source GUP001
[Debug]   [2023-12-20 13:13:44] -- no changes
[Info]    [2023-12-20 13:13:44] no match for target GUP001_TF_MNT in source
[Info]    [2023-12-20 13:13:44] no match for target GUP001_MNT in source
[Info]    [2023-12-20 13:13:44] no match for target GUP001_SG_ss_MNT in source
[Info]    [2023-12-20 13:13:44] no match for target GUP001_TF_ss_MNT in source
[Info]    [2023-12-20 13:13:44] no match for target GUP001_ss_MNT in source
[Info]    [2023-12-20 13:13:44] Writing to file (directory will be created if missing): 2021_CarlhoffNature.janno

I think we should slowly stop to talk about "individuals" when we refer to .janno rows. This will be a long and slow process, but we should to become more clear in the terminology here.

codecov[bot] commented 10 months ago

Codecov Report

Attention: 8 lines in your changes are missing coverage. Please review.

Comparison is base (d2dc568) 68.49% compared to head (7453873) 68.46%.

Files Patch % Lines
src/Poseidon/CLI/Jannocoalesce.hs 27.27% 4 Missing and 4 partials :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## jannocoalesce #284 +/- ## ================================================= - Coverage 68.49% 68.46% -0.04% ================================================= Files 26 26 Lines 3409 3412 +3 Branches 389 391 +2 ================================================= + Hits 2335 2336 +1 Misses 685 685 - Partials 389 391 +2 ```

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