hgvs c to p - handle case where there's a stop codon prior to the end of the coding sequence

[reece]

Originally reported by: Rudolph Rico (Bitbucket: rrico, GitHub: rrico)

---

Some transcripts contain stop codons preceding the end of the coding sequence, e.g. NM_020451.2

Mutalyzer does not return a result; hgvsc_to_hgvsp currently throws an exception; this should handle this case gracefully.

Suggestion: p.?

Links

• imported from: CORE-110 (Invitae access required)

---

• Bitbucket: https://bitbucket.org/biocommons/hgvs/issue/110

[reece]

Original comment by Rudolph Rico (Bitbucket: rrico, GitHub: rrico):

---

p.s. this came out the clinvitae data analysis (issue #102)

[reece]

Original comment by Rudolph Rico (Bitbucket: rrico, GitHub: rrico):

---

Checked in fix & tests; will report p.?. One note - this does end up creating some somewhat cryptic cases where a seemingly innocuous substitution would return p.?. There's no way to "annotate" that decision.

[reece]

Original comment by Rudolph Rico (Bitbucket: rrico, GitHub: rrico):

---

CI tests pass. Closing.

[reece]

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

---

Removing milestone: milestone 5 (automated comment)