v1.4.4

The correct files to download are dnmtools-1.4.4.tar.gz or dnmtools-1.4.4.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

• unxcounts works for sym files by @andrewdavidsmith in #225
• Verbose output for sym and xcounts by @andrewdavidsmith in #227
• More help info printed for roi command by @andrewdavidsmith in #228
• Adding cpgbins command by @andrewdavidsmith in #231
• roi accepts xsym input by @andrewdavidsmith in #235
• Yaml output for bsrate by @andrewdavidsmith in #237
• One-based variable-step bigWig in kmersites by @andrewdavidsmith in #238

Full Changelog: v1.4.3...v1.4.4

v1.4.3

What's Changed

• More uniform to command line arguments.
• Added compressed format for counts if many counts files most be stored (xcounts and unxcounts commands).
• Added commands to convert between counts files that have only covered sites or all sites (covered and recovered commands), which help when coverage is sparse, but all sites must be present when comparing files.
• More commands can accept compressed input files.
• Bugfixes.

New Contributors

• @punidramesh made their first contribution in #215

Full Changelog: v1.4.2...v1.4.3

v1.4.2

The correct files to download are dnmtools-1.4.2.tar.gz or dnmtools-1.4.2.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 amrfinder command has been optimized for performance with addition of multithreading
• Updating to help dnmtools build on conda servers for macos

Full Changelog: v1.4.1...v1.4.2

v1.4.1

The correct files to download are dnmtools-1.4.1.tar.gz or dnmtools-1.4.1.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 guessprotocol command was reworked to use a probabilistic model and generate more helpful output.
• The guessprotocol documentation was rewritten.
• Documentation for the roi command was improved.
• Fixed a bug in the pmd command introduced in v1.4.0, which crashed on "insufficient data" unless run in verbose mode.
• Added option to output in gzip format for sym and states commands.

Full Changelog: v1.4.0...v1.4.1

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

v1.3.0

The correct files to download are dnmtools-1.3.0.tar.gz or dnmtools-1.3.0.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 abismal command has been updated to output BAM format directly.
• Several checks have been added for input data format correctness across commands.
• Random numbers are controlled across environments for greater reproducibility.
• The uniq command can now tag each read with its duplicate count.
• Additional mlml and radmeth documentation.
• More automated tests available with make check.
• The states command now can use multiple threads.
• Several other commands have improved efficiency.

Full Changelog: v1.2.5...v1.3.0

v1.2.5

The correct files to download are either dnmtools-1.2.4.zip or dnmtools-1.2.4.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

• Speed improvements for the format, uniq and counts command when compressed file formats are used.

New Contributors

• @masarunakajima made their first contribution in #47

Full Changelog: v1.2.4...v1.2.5

v1.2.4

The correct files to download are either dnmtools-1.2.4.zip or dnmtools-1.2.4.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

• Optimizing duplicate remover by @andrewdavidsmith in #45
• Fixing a major bug in the format command from v1.2.3 (don't use that version!)

Full Changelog: v1.2.3...v1.2.4

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