Support NMD escape and triggering

[dglemos]

Description

In the current API to set a variant type with NMD_escaping we have to set the flag nmd_escape:

{
  "variant_types": [{
    "comment": "this is a comment",
    "de_novo": false,
    "inherited": true,
    "nmd_escape": false,
    "primary_type": "protein_changing",
    "secondary_type": "stop_gained",
    "supporting_papers": ["1"],
    "unknown_inheritance": true
  }]
}

This PR removes the flag nmd_escape.
The secondary_type should already include the full variant type: frameshift_variant_NMD_escaping, stop_gained_NMD_escaping, stop_gained_NMD_triggering, etc.

Important

This update requires a web update.

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JIRA Ticket

G2P-698

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Contributor Checklist

• The code compiles and runs as expected
• Relevant unit tests are added or updated
• All unit tests are passing
• Code follows the G2P Coding Guidelines
• Documentation (code comments, confluence, etc.) has been updated as needed

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Reviewer Checklist

Please follow the Code Review Guidelines when reviewing this PR.

• I have followed all review guidelines

[seeta-ramaraju]

Tested with web changes EBI-G2P/gene2phenotype_web#203