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@guilhermesena1 guilhermesena1 released this 01 Jul 23:36
· 89 commits to master since this release
v5.0.0
fa5f699

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.

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