"guess" at variant file format, if not obvious from filename

hammerlab / cohorts

Utilities for analyzing mutations and neoepitopes in patient cohorts

Apache License 2.0

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"guess" at variant file format, if not obvious from filename #232

Closed jburos closed 7 years ago

jburos commented 7 years ago

Quick hack to get around errors in #228 .. tried to infer file types from meta-data, but turned out to be too inconsistently formatting, surprisingly even among results from the same pipeline.

At any rate, this appears to work for now. With a sample size of one strelka & one mutect file, it appears that reading one file type as if it were the other fails in both directions.

coveralls commented 7 years ago

Coverage increased (+0.2%) to 53.496% when pulling c469841194708b6cb672a86a2883803cc72eb213 on fix-issue-228 into e61e9763bc0b64b2c728fffb08fc7a68e0a645ff on master.

coveralls commented 7 years ago

Coverage increased (+1.02%) to 54.308% when pulling de30ef2d4ba977480828175d70fe3c248fe18e0c on fix-issue-228 into e61e9763bc0b64b2c728fffb08fc7a68e0a645ff on master.