exentedRegion branch lineage functions and `parent_sequence`

[ssnn]

Review, document and add to master @milca tarshish 's functions that remain in branch extendedRegions. These are mostly lineage related functions. This will require coordination with @Kenneth Hoehn .

It would be good to add a function that fills the column parent_sequence for a repertoire data.frame. This column can be used in observedMutations, expectedMutations and calcBaseline to do the mutation analysis relative to the parent sequence in the lineage tree. Currently, to accomplish this, one needs to create a list an apply makeChangeoClone, buildPhylipLineage, makeGraphDf and bind_rows.

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[ssnn]

We have decided that the functions remaining in this branch, are basically wrappers and we are not going to add them. Also, if we were to add the plotting function, it should go to alakazam.