Bug fixes

Fixed corner-case rounding issues in several programs caused by inconsistent use of various rounding functions. They have been replaced by std::tr1::round.
Removed use of buffer for methcounts and allelicmeth leading to unpredictable memory usage by jackpot regions of unrealistically high coverage. This change has stabilized the memory usage of these two programs at 8GB for the human genome.
amrfinder no longer fails silently on incorrectly formatted epiread input files

Enhancements

methcounts now produces strand- and context-specific methylation levels and reports cytosines that have mutated away from the reference genome.
methcounts now has an option to produce only CpG methylation levels. This limits the output size from 25GB to 1GB for the human genome.
A new tool symmetric-cpgs is added under utils to merge information of symmetric CpGs so that the output of methcounts is compatible with other analysis tools.
levels now produces all information the methcounts statistics file contained as well as methylation levels for each cytosine context and mutation rate information.
methdiff now contains an option to restrict output to sites with nonzero coverage
methdiff output now is more consistent with methcounts output: changes detailed in the manual
library and merge-methylomes have been updated to reflect changes to methcounts output.

Substantial changes to the manual to highlight the change in usage of methcounts output with downstream analysis tools
A PDF copy of the manual is included in /docs.