The four functions:
getRefId provide reading access to data about
the present reference sequences in bamReader or bamWriter.
getRefData returns a
data.frame with three columns
(ID, SN, LN).
ID is the (0-based index which must be given when a
SN is the name of the sequence (e.g. chr1 for UCSC).
LN is the length of the reference sequence.
getRefCount returns the number of reference sequences.
getRefCoords returns a vector of coordinates which can be used to extract all stored aligns for this sequence from the
bamReader into a
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