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yatisht / usher

Ultrafast Sample Placement on Existing Trees
MIT License
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Bugfix and Reorganization #317

Closed jmcbroome closed 1 year ago

jmcbroome commented 1 year ago

This PR has two major inclusions:

First is a change I made a while back but didn't bring to the main repository before the holidays. I simply relocated the --node-stats option from the extremely bloated matUtils extract to the more appropriate matUtils summary and assigned it a single letter output option (-N, --node-stats).

Second, I've addressed the bug raised in https://github.com/yatisht/usher/issues/315. Thanks to Richard Neher for reporting the issue!

As a minor inclusion, I've added an attribute to the nextstrain JSON output that enables some additional features on nextstrain (https://github.com/yatisht/usher/issues/284).

jmcbroome commented 1 year ago

It looks like the ubuntu build failed because of a 503 service error when attempting to build the environment. Hm. I haven't seen that before with github workflows.

yatisht commented 1 year ago

I reran and it worked. Thanks.