John St. John

This PR addresses the new feature I mentioned in https://github.com/jettify/pytorch-optimizer/issues/385. Thank you for your time reviewing!

AdamD implementation (or option to skip bias-correction to adam-derived optimizers)?

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I recently put out a proposal to add an argument to adam-derived optimizers to skip the bias-correction term on `w`, only applying it to `v`. See the figure attached in...

rabix calling grep an extra time w/ no args for some reason

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My program using the ref implementations of grep and wc from the festival of genomics: ``` #!/usr/bin/env cwl-runner class: Workflow requirements: - class: ScatterFeatureRequirement inputs: - id: "#mutation" type: string...

Allow for reading in block gzip compressed VCF files.

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Block gzip compressed/indexed VCF files are currently mistaken for Parquet format, and an error like this is thrown: ``` dbsnp_132_b37.leftAligned.vcf.gz is not a Parquet file. expected magic number at tail...

Mutect implementation work

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An initial rough version of the MuTect algorithm, mostly ported over from work on Avocado. --- This change is [](https://reviewable.io/reviews/hammerlab/guacamole/394)

Work on getting Mutect algorithm up and running

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This PR is to track progress and collaborate on an implementation of the MuTect algorithm referenced in #114.

expose model.Record

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This allows for nice things like type annotations for functions that accept a `Record` as well as users building dummy `Record` objects for testing. For example I can now do...

# What does this PR do ? Adds two helpful items for working with ABCs that eventually get IOMixin: 1. A parent `NeedsIOMixin` ABC that lets you inform a parent...