PMUX-1652: [GENOMOD] update `dx extract_assay germline --retrieve-genotype` to retrieve `ref`, `half` (ref), and `no-call` genotype types

dnanexus / dx-toolkit

DNAnexus platform client libraries

http://autodoc.dnanexus.com/

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PMUX-1652: [GENOMOD] update `dx extract_assay germline --retrieve-genotype` to retrieve `ref`, `half` (ref), and `no-call` genotype types #1353

Closed csuloway-dnanexus closed 5 months ago

csuloway-dnanexus commented 5 months ago

Updated dxpy CLI tool dx extract_assay germline enable retrieval of ref, half (ref), and no-call genotype types when using the --retrieve-genotype flag.

Updated options for genotype filtering to include location and new genotype type options.
Added options --infer-ref and --infer-nocall to infer a genotype type excluded during dataset load.
Updated and added tests.

csuloway-dnanexus commented 5 months ago

We have hopefully addressed all of the comments. Please let us know if any more changes need to be made before merging into master. Thanks!