Merge pull request ga4gh#74 from sawmonaco/handle-hgvsdatanotavailabl…

…e-error-in-translation

Add error handling for HGVSDataNotAvailableError during HGVS translation

Merge pull request ga4gh#70 from GenomicMedLab/issue-69

Use SequenceInterval and LiteralSequenceExpression in ga4gh.vrs.extras.

This is good. A future issue to address: using vrs-python to automatically translate SimpleInterval -> SequenceInterval and State -> LiteralSequenceExpression.

add MANIFEST.in

Includes improvements to use of seqrepo data proxy.

Add support for VRS 1.2 Classes in _normalize_allele (ga4gh#57)

* wip: update _normalize_allele with vrs 1.2.0 classes

* Add tests for uncertain del/dup allele normalize

* Update _normalize_allele + tests

* PR Review: Switch on ival.type rather than exception

* PR Review: Separate ival and state types in _normalize_allele

* Remove notebook that was accidentally added

symlink vrs subrepo dependency

Closes ga4gh#54: Unpin python-jsonschema-objects

updated vrs to 1.2.0.rc1

note that vrs-python 0.7 corresponds to vrs 1.2

updated vrs submodule to 1.2.0.dev1