search

broadinstitute / gatk-protected

Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead
BSD 3-Clause "New" or "Revised" License
33 stars 20 forks source link

Write integration test for GermlineCNVCaller for single sample calling #1065

Closed asmirnov239 closed 7 years ago

asmirnov239 commented 7 years ago

@mbabadi could you do it?

sooheelee commented 7 years ago

Is the test <src/test/java/org/broadinstitute/hellbender/tools/coveragemodel/germline/GermlineCNVCallerIntegrationTest.java> not the integration test?

asmirnov239 commented 7 years ago

@sooheelee It's a collection of different tests, but it's missing some use cases

mbabadi commented 7 years ago

@asmirnov239 it covers PoN creation and calling (from the created PoN, and from the "exact" PoN). It certainly does not cover all combination of all advanced arguments, and we do not intend to do that either. Perhaps we should extend the test to include w/ and w/o ARD, and w/ and w/o bias covariates. I'm open to suggestions.

asmirnov239 commented 7 years ago

@mbabadi What I meant is to write an extra test for a use case of calling events on a single sample (as it is a requirement for our workflows). Just a single test with most generic arguments should suffice I think.

droazen commented 7 years ago

Issue moved to broadinstitute/gatk #3002 via ZenHub