Cannot parse HGVS NP_000095.2:p.Gly168_His169=

[markwoon]

When trying to parse NP_000095.2:p.Gly168_His169= I get:

Caused by: de.charite.compbio.jannovar.hgvs.parser.HGVSParsingException: org.antlr.v4.runtime.NoViableAltException
	at de.charite.compbio.jannovar.hgvs.parser.HGVSErrorStrategy.reportNoViableAlternative(HGVSErrorStrategy.java:11)
	at org.antlr.v4.runtime.DefaultErrorStrategy.reportError(DefaultErrorStrategy.java:136)
	at de.charite.compbio.jannovar.hgvs.parser.Antlr4HGVSParser.aa_change_inner(Antlr4HGVSParser.java:888)
	at de.charite.compbio.jannovar.hgvs.parser.Antlr4HGVSParser.aa_change(Antlr4HGVSParser.java:743)
	at de.charite.compbio.jannovar.hgvs.parser.Antlr4HGVSParser.aa_single_allele_single_change_var(Antlr4HGVSParser.java:372)
	at de.charite.compbio.jannovar.hgvs.parser.Antlr4HGVSParser.aa_single_allele_var(Antlr4HGVSParser.java:316)
	at de.charite.compbio.jannovar.hgvs.parser.Antlr4HGVSParser.hgvs_variant(Antlr4HGVSParser.java:201)
	at de.charite.compbio.jannovar.hgvs.parser.HGVSParser.parseHGVSString(HGVSParser.java:42)
	... 75 common frames omitted
Caused by: org.antlr.v4.runtime.NoViableAltException: null
	at org.antlr.v4.runtime.atn.ParserATNSimulator.noViableAlt(ParserATNSimulator.java:2026)
	at org.antlr.v4.runtime.atn.ParserATNSimulator.execATN(ParserATNSimulator.java:467)
	at org.antlr.v4.runtime.atn.ParserATNSimulator.adaptivePredict(ParserATNSimulator.java:393)
	at de.charite.compbio.jannovar.hgvs.parser.Antlr4HGVSParser.aa_change_inner(Antlr4HGVSParser.java:820)
	... 81 common frames omitted

This is with Janovar 0.34.

[holtgrewe]

Interesting. This refers to this part of the specification:

• http://www.hgvs.org/mutnomen/accepted001.html

Which we indeed have not considered so far.

[holtgrewe]

Actually, it should be. Looking further into this.

[holtgrewe]

OK, it has not been clearly documented but parsing HGVS is only fully implemented for nucleic acid sequences. The Antlr-based parser for amino acids is there but building Java objects has not been implemented yet.

#517 will fix this issue as "parsing" will work but it will return null. #516 documents explicitely that this is still missing.

I don't have the time to implement this (as I have no need for it right now) but would welcome and help with pull requests.