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.