GVS / Hail VDS integration test [VS-639] #8086
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mcovarr
requested review from
gbggrant,
rsasch,
koncheto-broad and
RoriCremer
and removed request for
gbggrant
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #8086 +/- ##
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Coverage ? 86.240%
Complexity ? 35200
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Files ? 2173
Lines ? 165041
Branches ? 17794
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Hits ? 142331
Misses ? 16382
Partials ? 6328 |
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RoriCremer
reviewed
Nov 9, 2022
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| script_url_prefix="https://raw.githubusercontent.com/broadinstitute/gatk/~{branch_name}/scripts/variantstore/wdl/extract" | ||
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| for script in hail_gvs_import.py hail_join_vds_vcfs.py gvs_vds_tie_out.py |
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this is clever, but it might be worth adding a comment somewhere about why we are doing this?
RoriCremer
reviewed
Nov 10, 2022
| RGQ: int32 | ||
| } | ||
| 'vds_entry': struct { | ||
| LGT: call, |
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Dont we also have a GT in the VDS? isn't that what messed us up? or do we need to drop it?
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Actually this appears to be correct as is.
RoriCremer
approved these changes
Nov 10, 2022
This was referenced Mar 17, 2023
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This ticket was intended as a spike but in the process of spiking I was able to create a peer Hail VDS integration test to the VCF integration test. This seems like a viable candidate for Q4 MVP so putting it out for review as is.
This creates a separate integration test for AoU Delta-style Hail VDS outputs with a tieout to regular GVS VCFs. The existing
GvsQuickstartIntegrationWDL has become an "uber" integration WDL that by default runs both the VCF and Hail VDS integration tests, but these can be toggled on or off separately with optional boolean inputs.