Error when "collapseByClone" is FALSE in calcDBClonalConsensus

[Ang Cui]

The db_ClonalConsensus variable is not defined unless collapsedByClone is TRUE

# If collapseByClone is TRUE then collapse the db by clones
if(collapseByClone){ 
    uniqueCloneIDs <-  unique(db[,cloneColumn])
    indexOfFirstOccurenceOfClone <- match(uniqueCloneIDs, db[,cloneColumn])
    db_ClonalConsensus <- db[indexOfFirstOccurenceOfClone, ]
    db_ClonalConsensus$CLONAL_CONSENSUS_SEQUENCE <- unlist(list_ClonalConsensus)
}

return(db_ClonalConsensus)

[Ang Cui]

Since the function name is calcDBClonalConsensus, we might as well make it always collapseByClone unless you have other concerns.

[Mohamed Uduman]

Fixed this. Ang, we do need the collapseByClone=FALSE flag if you want to retain all the individual sequences but still calculate the CLONAL_CONSENSUS_SEQUENCE.