Remove uses of VariantContextSetBuilder in all unit tests#819

Draft

kstromhaug wants to merge 17 commits intomainfrom ks_remove_variantcontextsetbuilder

+455-371

Commits on Mar 28, 2022

Remove use of VariantContextSetBuilder from ErrorRateByReadPositionTest.scala
Kari Stromhaug
committed
Remove VariantContextSetBuilder from ReviewConsensusVariantsTest.scala
Kari Stromhaug
committed
Remove VariantContextBuilder from VariantMaskTest.scala
Kari Stromhaug
committed

Commits on Mar 29, 2022

Remove a test that is no longer valid and fix another
Kari Stromhaug
committed
Fix one test and remove commented out code
Kari Stromhaug
committed

Commits on Mar 30, 2022

A few more changes to VariantMaskTest
Kari Stromhaug
committed
Fix VariantMask tests
Kari Stromhaug
committed
Most tests for AssessPhasingTest changed
Kari Stromhaug
committed
Start on next round of changes on AssessPhasingTest
Kari Stromhaug
committed
Just one test remaining in AssessPhasingTest
Kari Stromhaug
committed
Remove some comments in AssessPhasingTest and remove VariantContestSetBuilder in MakeMixtureVcfTest
Kari Stromhaug
committed
Remove some comments, remove VariantContextSetBuilder from MakeTwoSampleMixtureVcfTest
Kari Stromhaug
committed
Remove VariantContextSetBuilder from JoinVariantContextIteratorTest
Kari Stromhaug
committed
Remove and import
Kari Stromhaug
committed
Remove VariantContextSetBuider from ByIntervalListContextIteratorTest
Kari Stromhaug
committed

Commits on Mar 31, 2022

Fix UpdateVcfContigNames tests and remove one test in VariantMaskTest
Kari Stromhaug
committed

Commits on Apr 8, 2022

Fixed last few tests for contextsetbuilder
Kari Stromhaug
committed