MutationMention.toHGVS() returns '??' for entities already following the HGVS c. and m. notation
jhkbg opened this issue · 1 comments
It looks like MutationMention.toHGVS() returns '??' for recognized entities that already follow the HGVS nomenclature --- happens for entities in c. notation and m. only; and not for all.
Examples:
PMID 23560553, recognized entity=c.499C>A, normalized=c.499C>A, toHGVS() = ??
PMID 23588064, recognized=c.7148dupT, normalized=c.7148dupT, toHGVS() = ??
22288660 / m.16278C>T
23612258 / c.1431_1433dupAAA
However, this does not happen for other cases:
pmid=23588064, recognized=c.2071-2093del, norm=c.2071-2093del, tohgvs() = c.2071-2093del
23405979 / c.904-906delGAG
23623699 / c.300+1G>C
23732669 / c.1224_1225delCA
where it returns the right HGVS.
I'm not quite sure what the pattern is --- initially I thought it would return the correct toHGVS() for everything that was a range location ("c.1224_1225delCA") but a counter example is "c.1431_1433dupAAA" where it returns ??.
"m." are not considered by the "switch (type)" at the start of toHGVS().
(For structural abnormalities, toHGVS() also returns ?? but that's by design)
Added test cases here