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Hi (Herve),
I have been playing around with GappedAlignmentPairs and found it
pretty
useful. Some things that would be nice:
1) A method for getting the observed fragment length (would need to be
NA
when pairs are on different chromosomes). This should at least have an
option (if not always) to exclude the N cigar runs from the
calculation. Or
it could just take it from the TLEN (isize) column in the BAM file
(which
at least in the case of gsnap excludes the Ns).
2) A method called "introns" or something that returns the N regions
as a
GRangesList, as a complement to grglist(). Such a method would also be
nice
on GappedAlignments.
Thanks,
Michael
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