v1.4.0

The correct files to download are dnmtools-1.4.0.tar.gz or dnmtools-1.4.0.zip
Please do not download the "Source code" files. Those are generated by GitHub but lack certain files needed to build DNMTools.

What's Changed

• The bsrate command can now output bisulfite conversion per read in the form of a histogram.
• The counts command will now report all sites in all chromosomes from the reference genome even if they are not among the mapped reads (this responds to more than one user issue).
• Several of the commands now validate the input files, which should help in case two inputs get swapped.
• The selectsites command has a bug fix so it will not attempt to do binary search within compressed input files.
• The sym command now ensures sites are sorted; this is critical for making symmetric CpG sites, as doing this requires the C on both strands of a CpG to be consecutive.
• A new command, metagene, has been added. This generates plots of methylation levels around given genomic landmarks (e.g., transcription start sites) although the documentation will lag behind this release.
• The diff command can now compute the intersection of sites between two files in case they differ. The differential methylation levels are still only computed for sites present in both input files.
• The pmd, bsrate, hmr, selectsites and cleanhp commands can now generate additional summary data files.
• Bug fix in pmd: in some situations the final end of a PMD was allowed to go beyond the end of a chromosome; fixed now.
• The cleanhp command can now generate a histogram of the fraction of read pairs with each amount of matching assuming the pair is a hairpin (aka inverted duplication).
• The states and selectsites commands can now output gzip format.

Full Changelog: v1.3.0...v1.4.0