Cleaned up commandline arguments

openvax / topiary

Predict mutated T-cell epitopes from sequencing data

Apache License 2.0

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Cleaned up commandline arguments #57

Closed iskandr closed 8 years ago

iskandr commented 8 years ago

Every group of arguments now has its own package, which contains a function that adds arguments to a parser and helpers for using the argument values. This lets us repurpose subsets of Topiary's CLI for other libraries (like vaxrank).

Also added some column filtering and rename options for output files (since at least one user wants a custom output format: https://github.com/hammerlab/topiary/issues/56)

This change is

coveralls commented 8 years ago

Coverage decreased (-2.8%) to 85.396% when pulling 6462533d23a52bd3c175bf1aa7ebcd8e14b20007 on reorganize-commandline-args into 1d3d8d0758e97a758d360c92c2d30330d0fe1a98 on master.

coveralls commented 8 years ago

Coverage decreased (-3.6%) to 84.6% when pulling 36a38900be61c0461ce5e4a7f6a18c7a1707509f on reorganize-commandline-args into 1d3d8d0758e97a758d360c92c2d30330d0fe1a98 on master.

coveralls commented 8 years ago

Coverage decreased (-0.2%) to 88.0% when pulling 032c2920ac2450b71e2545987dbb76549b35a7d2 on reorganize-commandline-args into 1d3d8d0758e97a758d360c92c2d30330d0fe1a98 on master.

arahuja commented 8 years ago

Looks good! minor comments

coveralls commented 8 years ago

Coverage decreased (-0.1%) to 88.072% when pulling 5c12bab3d47bd86d396b079294aff141265f8b41 on reorganize-commandline-args into 1d3d8d0758e97a758d360c92c2d30330d0fe1a98 on master.