:feature:`-` Add possibility to constraint knn averaging: when turned on avoids edges between cells of specified groups
🐛`-` Fix an error in filter_cells: colors array is now filtered as well
:feature:`-` Improve the debug molecular report option to support hdf5
:feature:`-` It supports SmartSeq2 and has a new run_smartseq2 command
:feature:`-` It supports multiple bam files input, it can interpret the file(s) as either as one-file-one-cell or just as batches to be analyzed together. IMPORTANT: a cell cannot be distributed over different bamfiles!
:feature:`-` Generalized logic to include more layers than just Spliced, Unspliced, Ambiguous
:feature:`-`--without-umi option allows analyzing UMI-less data such as SmartSeq2
:feature:`-` support different verbosity levels with the -v flag
:support:`-`--multimap option was removed because it could have yield incorrect results depending on the output format chosen for the aligner
:feature:`-` Improved compatibility with InDrops and STRT through the --umi-extentions. It allows the same pipeline to be applied to methods with short molecular barcode that cannot be used call a unique molecule without the gene mapping information.
🐛`-` Sometimes velocyto missed to detect and warn the user that the .gtf genome annotation file was not sorted, this could have caused undetected errors in the analysis. If you run velocyto without sorting the .gtf, we suggest rerunning.
:feature:`-` CLI does not require presorting the gtf files. To reduce possibility of incorrect usage, now .gtf file sorting sorting is performed in memory (and not saved).
:feature:`-` Improve documentation: remove information about sorting .gtf files. This procedure is not needed anymore.
:feature:`-` Large parts of the documentation rewritten to match the changes in API
:feature:`-` Make the CLI simpler removing the extract interval step.
Now the source .gtf files can be provided directly, they should be provided sorted using sort -k1,1 -k7,7 -k4,4n -o [OUTFILE] [INFILE]