removed arrays code, renamed packages #7260
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On second thought -- to simplify the merge to master we may take a different approach (copying files, squashing, etc) so I'm updating the approach above for this PR |
RoriCremer
approved these changes
May 19, 2021
ahaessly
approved these changes
May 19, 2021
| @@ -178,8 +178,6 @@ public void onTraversalStart() { | |||
| case GENOMES: | |||
| vetTsvCreator = new VetTsvCreator(sampleIdentifierForOutputFileName, sampleId, tableNumberPrefix, outputDir); | |||
| break; | |||
| case ARRAYS: | |||
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do we even need this switch statement? we make the same call for both exomes and genomes
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Yes! I was restraining myself to clean up code and save that for the next PR. Mostly to make the review of this PR easy (ie it's all structural, you don't need to look at each line of code) and the next one smaller, but where the lines of code matter. We also have some "common" code that is now really tool specific that we can shift. Things like the above, etc.
This was referenced Mar 17, 2023
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Conceptually -- two things happen in this PR.
...gvs
|- ingest
|- filtering
|- extract
- common
All tests pass (can be run with
./gradlew test --tests "org.broadinstitute.hellbender.tools.gvs*"). I will run a full workflow in Terra (import, train, extract) and verifyBEFORE we merge, we'll the existing "ah_var_store" to indicate this is where array code lives