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Resolve "Ensure that all multiallelic blocks are complete"

Øyvind Evju requested to merge all-multiallelic-blocks-complete into dev

Description

Fixes issue #10 (closed)

Implement solution proposed in issue

Type of change

  • New feature
  • Breaking change
  • Bug fix
  • Improvement

Testing

  • Tests have been added that prove my fix is effective or that my feature works
  • Previous tests have been modified/removed
  • Testing done by manual inspection of results (specify)
  • Approved by customer (specify)
  • Unit tests and lint pass
  • CI tests pass (if applicable)

I have checked that blocks are added back, and that all blocks in the $OUTPUT_VCF are identical to the multiallelic blocks in the $VCF (from vt normalize) with the same identifiers, in a sample where this issue was present.

Other

Any risks? Are there points in the code the reviewer needs to double check or where you would like advice?

Checklist:

  • I have performed a self-review of my own code
  • My code and commit messages follows the style guidelines in Code Review checklist procedure
  • I have commented my code, particularly in hard-to-understand areas
  • My branch has recently been updated with new changes in dev (and tested) before this merge request
  • I have made corresponding changes to the documentation (state where)

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