add match cli

Author: nebfield

pgscatalog.matchapp/README.md

@@ -0,0 +1,31 @@
+# `pgscatalog-match`
+
+A CLI application that matches (intersects) variants in a normalised scoring file against variant information files. It outputs scoring files compatible with `plink2 --score`, a summary log, and a large match candidate information log.
+
+Various match strategies are used to generate a list of match candidates. These candidates are filtered by user parameters to produce up to one "best match"  variant for each variant in the original scoring file.
+
+Matching fails if not enough variants are present in the target variant information files. You can adjust `--min_overlap` to change the matching failure threshold, but it's not a good idea normally.
+
+The [PGS Catalog Calculator](https://github.com/PGScatalog/pgsc_calc) uses this CLI application internally. If you want to calculate polygenic scores using an automated workflow, the PGS Catalog Calculator is the best method to use.
+
+## Installation 
+
+```
+$ pip install pgscatalog-match
+```
+
+## Usage
+
+```
+$ pgscatalog-match ...
+```
+
+## Documentation
+
+See **link to docs**.
+
+## Help
+
+```
+$ pgscatalog-match --help
+```

pgscatalog.matchapp/poetry.lock

@@ -0,0 +1,3 @@
+[virtualenvs]
+create = true
+in-project = true

pgscatalog.matchapp/poetry.toml

@@ -0,0 +1,23 @@
+[tool.poetry]
+name = "pgscatalog-matchapp"
+version = "0.1.0"
+description = ""
+authors = ["Benjamin Wingfield <bwingfield@ebi.ac.uk>"]
+license = "Apache-2.0"
+readme = "README.md"
+packages = [
+    { include = "pgscatalog", from = "src" },
+]
+
+
+[tool.poetry.dependencies]
+python = "^3.11"
+"pgscatalog.matchlib" = {path = "../pgscatalog.matchlib", develop = true}
+
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^8.0.0"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"