ChangelogΒΆ

0.13.0 2018-01-19

  • [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).

0.12.4 2018-01-18

  • [Bug] #40: Error in hdf5 serialization when using cluster label as object array is now fixed

0.12.3 2018-01-17

  • [Bug] #38: Error in running run10x is now fixed

0.12.2 2018-01-12

  • [Bug] #37: Initial cell size array gets updated properly when filtering cells

0.12.1 2018-01-04

  • [Bug] #35: Attempted to fix a reported bug running velocyto CLI

0.12.0 2017-12-17

  • [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 multi10x
  • [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

0.11.0 2017-12-01

  • [Feature]: further ~5x speedup of cython functions making them 100% C and using malloc instead of memory views
  • [Bug]: The debug and sampleid option had the same short flag -d
  • [Bug]: fix a bug with ambiguous molecules counting and version bump

0.10.0 2017-11-18

  • [Feature]: Improve the docs
  • [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