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Releases: smithlabcode/methpipe
Releases · smithlabcode/methpipe
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 They have been replaced by std::tr1::round.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
andallelicmeth
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 underutils
to merge information of symmetric CpGs so that the output ofmethcounts
is compatible with other analysis tools. levels
now produces all information themethcounts
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 coveragemethdiff
output now is more consistent withmethcounts
output: changes detailed in the manuallibrary
andmerge-methylomes
have been updated to reflect changes tomethcounts
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 inmerge-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 tohypermr
to reflect its more general usage.- A PDF copy of the manual is included in
/docs
. merge-bsrate
,merge-methcounts
, andduplicate-remover
moved to the/utils
directory- Deprecated programs
reorder
andclipmates
have been removed. - Directories created for
mlml
andamrfinder
and related programs to differentiate standalone published tools from coremethpipe
functions.
methpipe-3.1.1
Samtools (version 0.18) and smithlab_cpp are included.