v5.0.1

** Please make sure to download files methpipe-5.0.1.tar.gz or methpipe-5.0.1.zip and not the "Source code" files provided automatically by github, as these do not contain all necessary files for compilation. **

This release is identical to versioon 5.0.0 (smough) with the exception of the removal of deprecated files (namely htslib_wrapper_deprecated.*pp under src/smithalb_cpp).

smough

This major release of methpipe changes the first steps in the pipeline by directly accepting the SAM/BAM inpute file from a wide range of mappers. In continuation of release 4.1.2-alpha, we have discontinued the to-mr function to replace it with format_reads, which standardizes SAM formats from different mappers to an output that is understandable by the subsequent methpipe tools.

The new pipeline, which describe each tool available on methpipe, is documented in the manual under docs/methpipe-manual.pdf. In it, we describe how to map reads to a FASTA reference genome using abismal.

Besides the transition to SAM input, we have addressed the following issues:

• Issue #161 was fixed, where compiling with clang (used by default in the Mac OS) was failing in several programs that reported "bad input"
• Issues #177 , #183 and #184 were addressed where FASTA files that contained spaces were causing problems in methcounts. FASTA inputs can have arbitrary read names as long as the first word of each chromosome is unique.
• Issue #180 has been fixed, and users can now set LDFLAGS and CPPFLAGS when cloning the repository from source

*** Please make sure to download files methpipe-5.0.0.tar.gz or methpipe-5.0.0.zip and not the "Source code" files provided automatically by github, as these do not contain all necessary files for compilation.

v4.1.2-alpha

This is a pre-release that focuses on full transition from MR to SAM file format. Much of the functionality of 4.1.2 is similar to 4.1.1, but mr files are no longer supported. This means some major changes in installation and the downstream pipeline:

• HTSLib is no longer an optional dependency. Installation of the htslib can be done through apt, brew or by following the installation guidelines. HTSLib is used for BAM file decompression, so BAM and SAM files can be used interchangeably.

• we recommend mapping reads using the new abismal software tool, which generates SAM output.

• to-mr is replaced by format_reads, and must be run both on abismal outputs and in SAM files generated by other mappers. This tool converts paired-end reads to single-end by merging mates, and also formats the single-end mapped reads to a standardized format used by downstream tools. SAM files generated by other mappers can similarly be provided as input, but the mapper of origin must be specified with the -f flag (currently supported mappers are abismal, bismark and bsmap)

• bsrate, duplicate-remover, methcounts and methstates now use the formatted SAM files as input.

Changes to the pipeline are documented at the methpipe manual under docs/methpipe-manual.pdf

Once the methcounts program generates the resulting .meth files, the commands to run subsequent pipeline programs remain virtually the same.

*** Please make sure to download files methpipe-4.1.2.tar.gz or methpipe-4.1.2.zip and not the "Source code" files provided automatically by github, as these do not contain all necessary files for compilation.

fullmoonlizard

This version is the same as 4.1.0, but fixes a problem with the MappedRead class that was crashing programs that used them.

Update: Please only download the numbered release, as the other two zip files are created by the GitHub release system as an archive of source, and will not have all the files needed to build and use methpipe. We have tried several work-arounds to prevent GitHub from creating those zip files when we tag a commit to make a release, but so far the best work-around is to ask you (presumably the user) to ignore those files.

moonlizard

This minor release (4.1.0) includes the functionality added to major release 4.0.0, but should be much easier to build and install.

4.0.0-beta

• This version may be unstable
• Major feature added is capacity for reading gzip format in many tools
• Code now links to HTSlib for any BAM/SAM format I/O (optional)
• This version requires that the smithlab_cpp library is built separately (likely will be changed in future release).

v3.4.3

Bug fixes

• Fixed a bug in the dmr program, which used to report fewer DMR regions than it should be.

Enhancements

• The methcounts format now allows user-specified header lines, starting with "#", to provide more information. All downstream programs are compatible with the header now.
• The manual is updated with the information of the new WGBS mapper walt.
• The whole package is now based on C++11, allowing future enhancements.

v3.4.2

Bug fixes

• Release to maintain compatibility with the smithlabresearch website: the compressed source code provided with github releases does not include submodules, rendering it uncompilable. Please download methpipe from the website or clone the developmental version.

  Enhancements

• Minor additions to the manual

v3.4.1

Bug fixes

• Fixed bug in methcounts caused by improperly checking for write-privileges before opening output file stream

methpipe-3.4.0: Tuco

Bug fixes

• Fixed bug in bsrate causing abort while processing reads that hang over the end of a chromosome (and added warning message).
• The mutation tracking in methcounts introduced a bug in merge-methcounts when parsing mutated contexts. merge-methcounts now only counts non-mutated site information and doesn't break while parsing mutated contexts.
• duplicate-remover statistics tracking now functions properly: previously the good_bases_out value was not correct when using the sequence info option.
• allelicmeth no longer throws a "could not convert" exception when converting the index of the last CpG back to genomic coordinates.
• hmr and pmd no longer skip the last domain of each chromosome
• merge-bsrate output now includes previously omitted headers, consistent with bsrate output
• Fixed hypermr numerical issues by renormalizing learned posterior and transition probabilities at each iteration of the Baum Welch training.
• to-mr now ignores discordant pairs

Enhancements

• WALT, our new space-seeded wildcard bisulfite read mapper, has been integrated into our manual as the de facto mapper in methpipe. It can be cloned from https://github.com/smithlabcode/walt
• radmeth, a recently developed tool for multi-factor, multi-replicate differential methylation analysis, has been integrated into methpipe. A detailed description of the functionality is available in the manual.
• bigwig_to_methcounts.py introduced as a tool to convert tracks downloaded from MethBase on the UCSC genome browser to methcounts format. A description is in the manual.
• methcounts memory usage halved and now prints estimate of memory usage for each chromosome
• methcounts now prints every cytosine in the reference by default, even if an entire chromosome is not covered, to maintain line number consistency across samples
• merge-methcounts now provides an option to output the merged methylomes in a table format for easy piped downstream analysis. It now prints a union of CpG sites from its input files, even though the number of CpG sites for each file is different.
• roimethstat memory usage reduced drastically by loading only CpGs within target regions into memory.
• Added option to hmr to specify random number generator seed, allowing user to exactly reproduce results if necessary.
• hmr now reports the "effective genome proportion," the percentage of the genome not in deserts, in the verbose output.
• hmr no longer has nondeterministic behavior.
• levels output format is slightly changed. Now it is technically in YAML format.

Organizational changes

• Substantial changes to the manual to introduce WALT as our new standard read mapper
• Removed experimental directory build from makefile to prevent user use of programs that are not rigorously tested or production-ready
• Some outdated and MethBase related stuff were removed.