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hammerlab / hlarp

Normalize HLA typing output.
Apache License 2.0
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Reform compare argument parsing #27

Closed rleonid closed 7 years ago

rleonid commented 7 years ago

This PR fixes #23 by changing the format of compare arguments. The TL;DR is

hlarp compare optitype=/path/to/opti_dir athlates=/path/to/ath_dir ...

instead of

hlarp compare --optitype /path/to/opti_dir --athlates /path/to/ath_dir ...

this mostly simplifies some internal logic. There is also a small bug fix for dealing with samples that have no comparisons.

rleonid commented 7 years ago

I'm going to hold off on merging this until @ihodes comes back and has a chance to comment on the target branch.

rleonid commented 7 years ago

Sorry, @ihodes , I forgot and merged that branch. I'll merge this one too. Feel free to comment later.