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Merged
kathrynmurie merged 171 commits into from
Sep 23, 2025
Merged

Develop #44

kathrynmurie merged 171 commits into from
Sep 23, 2025

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@kathrynmurie
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@kathrynmurie kathrynmurie commented Sep 23, 2025

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kathrynmurie and others added 30 commits July 12, 2024 18:22
@kathrynmurie
Add directory and script to start from
1a90e5f
@kathrynmurie
Merge pull request #4 from PlasmoGenEpi/setup_repo_structure
fdf1ed8 
Add directory and script to start from
@nickjhathaway
Updated README; added conda env file; added tool excel_meta_to_json_m…
5a07208 
…eta.py;
@kathrynmurie
Merge pull request #5 from PlasmoGenEpi/add_example_datasets
2ca17c6 
Add dada2 clusters example
@kathrynmurie
add functions to create microhaplotype json from table
e9f0cf7
@nickjhathaway
added utils folder and extractor folders; started base class;
011b069
@nickjhathaway
Merge branch 'develop' of github.com:PlasmoGenEpi/pmotools-python int…
c773118 
…o develop

* 'develop' of github.com:PlasmoGenEpi/pmotools-python:
  Add dada2 clusters example
@kathrynmurie
Seperate functions from scripts
21fc571
@nickjhathaway
no message
0af4896
@nickjhathaway
added microhap tab to json to runner;
787e272
@nickjhathaway
Merge pull request #6 from PlasmoGenEpi/dada2_to_json
305ba5b 
Haplotype table to json
@nickjhathaway
adding misc utilities; tweaked current tools; added sphinx documentat…
05fcb94 
…ion;
@nickjhathaway
no message
ad81a36
@nickjhathaway
added an extraction tool for input into dcifer;
926ecf8
@nickjhathaway
optimizing pmo exporting code;
fc00c90
@nickjhathaway
added pmo_checker;
2bbb6f4
@nickjhathaway
modified scripts to be able to generate allele table with optional ad…
de4c38b 
…ditional columns;
@nickjhathaway
fixed typo in REAME.md; added some more required fields;
788533f
@nickjhathaway
adding some documentation;
935bbdb
@nickjhathaway
fix for changing how the representative_haps_ids have their IDs;
f4d39d6
@nickjhathaway
fix to use the input locus column name as opposed to the hard coded l…
b69d4ba 
…cous name;
@nickjhathaway
some renaming and typo fixes;
17e614d
@nickjhathaway
added PMO combiner for same panel but different sequencing analysis r…
eb72d11 
…uns;
@nickjhathaway
finished adding in combine_pmos;
5f3e55e
@nickjhathaway
added PMO writer; added counting of meta fields; added PMO extractor …
70a26ef 
…for filtering for meta fields;
@nickjhathaway
additional tools for extracting subsets of the PMO;
4da1df1
@nickjhathaway
analysis_name changed to pmo_name; abstracted out meta field extraction;
a73818b
@nickjhathaway
updates to generating simple counts from PMO; update for terra to pmo…
fdc467a 
… convertor;
@nickjhathaway
update documentation;
9d824e1
@nickjhathaway
no message
0c5e260
kathrynmurie and others added 25 commits September 19, 2025 15:20
@kathrynmurie
Resolve merge conflict
d520189
@kathrynmurie
Remove unused libraries and less strict on versions
543292c
@nickjhathaway
Merge pull request #37 from PlasmoGenEpi/feature/add_uv_project
15bc6c2 
Feature/add uv project
@kathrynmurie
Add pre-commit and update files to comply
1acecc2
@kathrynmurie
Add pre-commit to run on PR
19ac01d
@kathrynmurie
Remove schema being explicitly included
30be0e9
@kathrynmurie
Install pre-commit in action
d61eb6e
@kathrynmurie
Add precommit to dependencies
cad97d1
@kathrynmurie
Rename test yml CI
c986bea
@nickjhathaway
Merge pull request #39 from PlasmoGenEpi/feature/add_precommit
2bdb9a1 
Add pre-commit and update files to comply
@kathrynmurie
Add action to publish package
0e6172d
@nickjhathaway
moved scripts directory into project; added a cli.py which can be ins…
0d90b80 
…talled when doing pip install and installs as pmotools-python;
@nickjhathaway
update conda environment file;
c239328
@kathrynmurie
Merge branch 'develop' into feature/publish_on_tag
3e51558
@nickjhathaway
make sure pip and python installed;
cd03e28
@nickjhathaway
updated README.md;
ff1013d
@nickjhathaway
update for schema location;
a20077a
@nickjhathaway
updated schema, adding TravelInfo and updating numerical fields that …
2f14f92 
…should always be positive with setting minimums;
@kathrynmurie
Merge pull request #41 from PlasmoGenEpi/feature/move_scripts_structure
fad128e 
move scripts structure
@kathrynmurie
Update version
cbc2876
@nickjhathaway
Merge pull request #40 from PlasmoGenEpi/feature/publish_on_tag
a5f0485 
Add action to publish package
@nickjhathaway
updated output;
7abcd26
@kathrynmurie
Add option to have multiple bioinf ids in build
d54b4e9
@kathrynmurie
Merge pull request #42 from PlasmoGenEpi/hotfix/fix_allele_table_export
abf0f3e 
updated output to be library_sample_name instead of specimen_name
@nickjhathaway
Merge pull request #43 from PlasmoGenEpi/hotfix/update_bioinfo_run_as…
0862bd5 
…_col

Add option to have multiple bioinf ids in build
@kathrynmurie kathrynmurie merged commit 6db4a20 into main Sep 23, 2025
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3 participants

@kathrynmurie @nickjhathaway