getGene returns first not Not Localized results

[ssnn]

If there are ties and first=TRUE, getGene should return the first non "Not Localized" results. If there are only "Not Localized" calls, then return them. May add a new argument, "not.localized.omit"

Currently:

v_call <- "IGHV03-NL1,IGHV03-30_3,IGHV03-30"
getGene(v_call, first=TRUE)
[1] "IGHV03-NL1"

Wanted:

v_call <- "IGHV03-NL1,IGHV03-30_3,IGHV03-30"
getGene(v_call, first=TRUE)
[1] "IGHV03-30_3"

v_call <- "IGHV03-NL1,IGHV03-NL2"
getGene(v_call, first=TRUE)
[1] "IGHV03-NL1"

[ssnn]

How about adding omit_nl=FALSE (default) to getSegment(). Probably just needs an initial pass with a special regex.

[Jason Vander Heiden]

Done in 26be4b3 via omit_nl flag.