NEWS.md

In robinweide/tagmeppr: A computational pipeline to map tagmap-insertions

tagmeppr 0.2

• [x] results-method to make a df of results
• [x] updated results-metadata to be more clear (orientation is now strand info)
• [x] plotInsertions now handles failed experiments without insertions
• [x] counts are now correct: align() did show some duplicate reads (which were not remove due to strand-info)
• [x] added the option to use padding in findInsertions(), which fixes issues with the mapper reporting matches over the TIS.
• [x] wrote checkPrimer to... check... the... primers...
• [x] findInsertions() now uses D_scores to set orientation as strand
• [x] findInsertions() uses the 5rev_3fwd-flag for setting the orientation
• [x] plotInsertions() has better spacing, colours and handles orientation.
• [x] results() now enables filtering on pvalue, counts and orientation
• [x] plotSite() is ready to use and also shows the orientation
• [x] a bug plotSite() regarding x-ticks is fixed
• [x] Write readme
• [x] checks if bwa and samtools are found
• [x] Removed the weird NA-warnings for emperical center in align()
• [x] PCR-duplicates are now removed on demand with align(dedup = T)
• [x] overhauled findInsertions(): handles failed experiments and outputs correct orientation

tagmeppr 0.1

• [x] re-wrote indexing part to use internal ITRs
• [x] made classes for the index and the samples
• [x] packages is fully build-passed (without warnings) with travisCI
• [x] no longer need a fai: it is made internally w/ seqinfo
• [x] empirical center auto on 1K-Npad
• [x] correctly export methods
• [x] put postalign inside align
• [x] made a minimised fastq-seq to speed things up
• [x] made nice print methods

robinweide/tagmeppr documentation built on Feb. 26, 2020, 10:41 p.m.