v1.4.0
andrewdavidsmith
released this
30 Sep 01:00
·
293 commits
to master
since this release
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
andcleanhp
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
andselectsites
commands can now output gzip format.
Full Changelog: v1.3.0...v1.4.0