Unclear validation error for intronic variants mapped to processed transcripts

[reece]

Originally reported by: Kevin Jacobs (Bitbucket: bioinformed, GitHub: bioinformed)

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NM_153818.1:c.600+1G>A references an intronic variant, but it mapped to a processed transcript. Mutalyzer gives a fairly clear validation failure message:

#!python
Intronic position given for a non-genomic reference sequence.

while hgvs gives a less clear message:

#!python
Variant reference does not agree with reference sequence

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• Bitbucket: https://bitbucket.org/biocommons/hgvs/issue/213

[reece]

Original comment by Reece Hart (Bitbucket: reece, GitHub: reece):

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closes #213: clarify warning message when validating intronic variants