methpipe-3.3.0: Krazy8

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 They have been replaced by std::tr1::round.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.

Organizational changes

• 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.

methpipe-3.2.0 "punisher"

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.

Organizational changes

• 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.

methpipe-3.1.1

Samtools (version 0.18) and smithlab_cpp are included.