- [Bug]: Fix a bug that caused extremely slow runtimes when the input bam was not position sorted. Now velocyto will raise an error and ask the user to sort the file using samtools.
- [Support]: Improve the changelog structure
- [Bug]: A change in slicing related to an API change of __getattr__ in loompy2
- [Bug]: Catch another error due to the API change of .create in loompy2
- [Bug]: Fix an incompatibility with loompy2 related to column and row attributes changing from dict to an object
- [Bug]: Catch error due to the API change of .create in loompy2
- [Feature]: Sample metadata file can be specified with different csv formats (the format will be determined automatically)
- [Feature]: Improve documentation: remove information about sorting .gtf files. This procedure is not needed anymore.
- [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).
- [Bug]: 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.
- [Bug] #40: Error in hdf5 serialization when using cluster label as object array is now fixed
- [Feature]: Pipeline now consider all the possible transcript models that could be supported by a set of reads individually and then decides on the spliced/unspliced/ambigous count.
- [Feature]: Support different Logic levels
- [Feature]: Changelog added to the doc
- [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]
- [Feature]: Large parts of the documentation rewritten to match the changes in API
- [Feature]: Remove the subcommand
- [Feature]: Add possibility to export pickle containing information of every molecule
- [Bug] #31: Memory usage bug should be solved.
- [Bug]: Many small bug fixes
- [Bug]: Incorrect 0-based indexing for splicing junction corrected (was not causing problems because buffered by MIN_FLANK)
- [Support]: Update the documentation for the new CLI
- [Bug]: fix a bug with ambiguous molecules counting and version bump
- [Bug]: The debug and sampleid option had the same short flag -d
- [Feature]: further ~5x speedup of cython functions making them 100% C and using malloc instead of memory views
- [Feature]: Add support for DropSeq pipelines where the barcode flags in the bam file are XC and XM instead of CB and UB
- [Bug]: Using sphinx 1.7 sorts the autodoc API correctly
- [Feature]: Improve the docs