BAM/SAM operations
------------------

This section will describe utility functions for manipipulating BAM files, using functions based on the `Rsamtools`_ package.

.. _Rsamtools: http://www.bioconductor.org/packages/release/bioc/html/Rsamtools.html

read.bam

bam.cov.gr

bam.cov.tile.st

bam.pair.cov

counts2rpkm

get.pairs.grl

count.clips

varbase

varcount

mafcount

splice.cigar

gc_content

bamtag


