Bug fixes

Fixed strand error for methcounts when dealing with 0 coverage sites at the tail of chromosomes. This prevents an error in merge-methcounts.
Removed some unused variables to prevent unnecessary compilation warning messages.
Fixed compilation error in Mac OSX 10.9 Mavericks caused by samtools dependency.
Fixed a bug in to-mr when the input file name does not have an extension.
Fixed silent failure in amrfinder when no AMRs were found
Fixed a bug in amrfinder related to conservatively biased likelihood values in low coverage samples.
Fixed a bug in amrfinder related to the likelihood penalty for imbalanced alleles

Enhancements

merge-methcounts now reports more specific error message when input files are not synchronized.
The manual now describes usage of the following programs: methentropy, fastLiftOver.

hmr_plant has been renamed to hypermr to reflect its more general usage.
A PDF copy of the manual is included in /docs.
merge-bsrate, merge-methcounts, and duplicate-remover moved to the /utils directory
Deprecated programs reorder and clipmates have been removed.
Directories created for mlml and amrfinder and related programs to differentiate standalone published tools from core methpipe functions.