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iossifovlab / gpf

GPF: Genotypes and Phenotypes in Families
MIT License
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External demo annotator #656

Closed IvoTod closed 4 months ago

IvoTod commented 4 months ago

Background

We decided to create a demo annotator to begin experimenting with integrating third party tools into our annotation pipeline.

Aim

Create a demo annotator with an external tool which measures the length of a given annotatable.

Implementation

The annotator classes used for this are called adapters and are built around calling another tool via subprocess. The first adapter uses a custom demo tool made for calculating the length of an annotatable. This is in a new package in GPF called external_demo_annotator and the tool is available in the CLI when installed as annotate_length and the annotators can be added to a pipeline. The 2 annotator types added are external_demo_annotator and external_demo_stream_annotator

lchorbadjiev commented 4 months ago

Please consider squashing and reorganizing commits before merging