Added the loadSecondaryAligns argument to tx_load_bam() so that secondary alignments can be easily discarded by setting it to FALSE. The same effect can be accomplished by inputing a scanFlag built with the Rsamtools::scanBamFlag() helper, but this way it is a more streamlined feature.
txtools 1.0.4
Added tx_combineTxReads() to combine reads processed by tx_reads().
Added ignore.strand functionality to load reads regardless if the RNA-seq library is strand-aware.
New plotting function tx_plot_numeric(): Plots numeric variables along the transcriptomic space.
tx_metagene_() functions have a normalization argument which yields the are under the curve to be proportional to 1(transcriptomic window length).
Plus minor fixes.
txtools 0.0.8
Fixed loading paired end BAM files when strand sign is defined by read2 (“last”).
Bugs fixed
Minor improvements:
Loading genome name as first word separated by spaces
Edited main vignette tutorial “txtools”
Added bam2txDT.R script in inst/ dir
Patch 0.0.8.1:
Added “splicingSite” option to tx_get_metageAtCDS() and tx_plot_metageneAtCDS().
txtools 0.0.7
General Update
Added vignette “txtools_user_guide”
Changed tx_add_diffNucToRef() for tx_add_misincCount()
Changed tx_add_diffNucToRefRatio() for tx_add_misincRate()
Fix minor bugs
0.0.7.4 patch: Fixed a bug that incorrectly included alignments with N operations in their CIGAR strings (gaps), that didn’t match the gene structure.
Removed plotly conversion in tx_plot_*() functions. As can be easily done by the user with plotly::ggplotly()
0.0.7.8 patch: Fixed tx_orderDT() so that order is not affected by levels in the ‘gene’ factor; accordingly fix tx_unifyTxDTL() so DTs have the same txcoor order. Changing name of function tx_add_misincorpRateNucSpec() in favor of tx_add_misincRateNucSpec(), so that it conforms to other function names, former can be used as alias but has been deprecated.
txtools 0.0.6
Fixed a bug detected when loading BAM files with mappings with empty sequence field
0.0.6.2 patch: Fixed bug related with spurious paired-end alignments, R1 and R2 order is wrong.
txtools 0.0.5
Update Bioconductor remotes.
Adding tx_core_mc() which is deprecated as alias of tx_reads().
Fix bug in tx_complete_DT() which added refSeq before necessary.
txtools 0.0.4
Uni and Multi-core functions merged into unique functions capable of using multi-cores with the parallel package.
txtools 0.0.3
Bug fixed when using BED6 annotation
txtools 0.0.2
Updating plotting function tx_plot_staEndCov() to remove coverage counts.
