- results-method to make a df of results
- updated results-metadata to be more clear (orientation is now strand info)
-
plotInsertionsnow handles failed experiments without insertions - counts are now correct:
align()did show some duplicate reads (which were not remove due to strand-info) - added the option to use padding in
findInsertions(), which fixes issues with the mapper reporting matches over the TIS. - wrote checkPrimer to... check... the... primers...
-
findInsertions()now uses D_scores to set orientation as strand -
findInsertions()uses the 5rev_3fwd-flag for setting the orientation -
plotInsertions()has better spacing, colours and handles orientation. -
results()now enables filtering on pvalue, counts and orientation -
plotSite()is ready to use and also shows the orientation - a bug
plotSite()regarding x-ticks is fixed - Write readme
- checks if bwa and samtools are found
- Removed the weird NA-warnings for emperical center in
align() - PCR-duplicates are now removed on demand with
align(dedup = T) - overhauled
findInsertions(): handles failed experiments and outputs correct orientation
- re-wrote indexing part to use internal ITRs
- made classes for the index and the samples
- packages is fully build-passed (without warnings) with travisCI
- no longer need a fai: it is made internally w/ seqinfo
- empirical center auto on 1K-Npad
- correctly export methods
- put postalign inside align
- made a minimised fastq-seq to speed things up
- made nice print methods