refactoring for testablity

[kcibul]

Code refactoring for better testability as part of the spanning deletions work that is being shelved.

Refactoring Changes
One of the challenges with this PR was testing as the work is really done in the lower-level methods and it would be nice to have this as a unit test rather than an integration/end-to-end test. This motivated the following changes:

• don't write to VCF directly, instead have take a Consumer to emit VariantContexts. This lets us provide a different consumer in unit tests to collect our result.
• we previously had a chain of calls createVariantsFromSortedRanges -> processSampleRecordsForLocation -> finalizeCurrentVariant that returned void and as a side effect wrote to VCF. These deeper methods now return a VariantContext and the writing (via consumer) is done higher up in the call stack
• made some private methods package-private so we could call them from tests

[codecov]

Codecov Report

❗ No coverage uploaded for pull request base (ah_var_store@8781b56). Click here to learn what that means.
The diff coverage is n/a.

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[gbggrant]

Looks good to me.