Cannot parse HGVS repeats

[markwoon]

I am getting errors parsing HGVS repeats. For example, attempting to parse NC_000014.8:g.101179660TG[14] gives me:

line 1:25 mismatched input '[' expecting {NT_STRING, NT_MINUS, NT_PLUS}
java.lang.NullPointerException: null
	at de.charite.compbio.jannovar.hgvs.parser.Antlr4HGVSParserListenerImpl.exitNt_change_substitution(Antlr4HGVSParserListenerImpl.java:404)
	at de.charite.compbio.jannovar.hgvs.parser.Antlr4HGVSParser$Nt_change_substitutionContext.exitRule(Antlr4HGVSParser.java:3121)
	at org.antlr.v4.runtime.Parser.triggerExitRuleEvent(Parser.java:408)
	at org.antlr.v4.runtime.Parser.exitRule(Parser.java:642)
	at de.charite.compbio.jannovar.hgvs.parser.Antlr4HGVSParser.hgvs_variant(Antlr4HGVSParser.java:219)
	at de.charite.compbio.jannovar.hgvs.parser.HGVSParser.parseHGVSString(HGVSParser.java:42)

This HGVS string comes directly from the examples section of the HGVS docs.

I'm using version 0.34.

And looking at the API for NucleotideShortSequenceRepeatVariability, it looks like there's no way to get the repeated sequence. Is this intentional, or am I missing something?

[holtgrewe]

Right now we only support a very limited number of repeats. From the grammar:

/** nucleotide short sequence repeat variability */
nt_change_ssr
:
	(
		nt_point_location
		| nt_range
	) NT_PAREN_OPEN NT_NUMBER NT_UNDERSCORE NT_NUMBER NT_PAREN_CLOSE
;

which means, e.g., <ref>:<spec>.<pos><seq>(<number>_<number>).

Adding this would require some expertise in Antlr development and knowledge of HGVS. It's not super hard work but right now I cannot invest the time into this. I'd welcome help with this, cf. #519.