v1.2.3

Major BUG in this release. Move to v1.2.4 instead.

The correct files to download are either dnmtools-1.2.3.zip or dnmtools-1.2.3.tar.gz

Please do not download the "Source code" files automatically generated by github, as they do not contain all files necessary for compilation.

What's Changed

• Update format command so that it can guess whether paired-end read names have a suffix (e.g., ".1" and ".2") that should be removed from read names to determine if the reads are mates.
• Fixed a bug in the diff command that broke the check for whether the sites were sorted in the same order for the two files being compared.

Full Changelog: v1.2.2...v1.2.3

v1.2.2

The correct files to download are either dnmtools-1.2.2.zip or dnmtools-1.2.2.tar.gz

Please do not download the "Source code" files automatically generated by github, as they do not contain all files necessary for compilation.

What's Changed

• improving functions for binary search inside counts files impacting roi and selectsites commands
• several checks for chromosomes sorted and consistent order of chromosomes impacting counts, bsrate and merge commands
• now the sym command does not act based on the mutation marker for sites, but still preserves it
• input files for reference genomes now mostly require that a single file include all chromosome sequences (impacts counts and bsrate)
• fix: bug in binomial confidence interval calculations used in levels
• fix: bug in levels output for certain non-CpG cytosines
• fix: Suggested fix for: radmeth-adjust replaces significant p-values by @iromeo in #32

Contributors

• @iromeo @andrewdavidsmith @guilhermesena1

Full Changelog: v1.2.1...v1.2.2

v1.2.1

The correct files to download are either dnmtools-1.2.1.zip or dnmtools-1.2.1.tar.gz
Please do not download the "Source code" files automatically generated by github, as they do not contain all files necessary for compilation

This is a patch release to update the version of abismal to v3.1.1 within dnmtools.

v1.2.0

The correct files to download are either dnmtools-1.2.0.zip or dnmtools-1.2.0.tar.gz
Please do not download the "Source code" files automatically generated by github, as they do not contain all files necessary for compilation

This release contains the following changes:

• Update to include abismal v3.1.0
• Bugfix in the selectsites command when using "on disk" mode
• Functionality in the merge command to retain info about a predicted mutation
• Updates to documentation

dnmtools-1.1.0

Please make sure to download files dnmtools-1.1.0.tar.gz or dnmtools-1.1.0.zip and not the "Source code" files provided automatically by GitHub, as these do not contain all necessary files for building the software.

New in 1.1.0:

• Documentation has been expanded
• The merge command can now generate files that are suitable as input to radmeth

dnmtools-1.0.0

Please make sure to download files dnmtools-1.0.0.tar.gz or dnmtools-1.0.0.zip and not the "Source code" files provided automatically by github, as these do not contain all necessary files for compilation.

First release of dnmtools.