Changelog

Changes in v0.5.6

(versions 0.5.5.2-4 were minor versions involving different testing frameworks)

  • fix typo in plotutils.clustered_sortind
  • support for versions of pysam expecting string (rather than unicode) for chromosome
  • support for cells in 2x2 tables with 0 items
  • lots of improvements to testing framework – now using docker on travis
  • added fisher as an explicit requirement
  • handle bx-python 0.7.3 which does not work correctly on bigbed files. A NotImplementedError is raised in this case. The workaround is to convert bigBed to BED (bigBedToBed program from UCSC; conda install -c bioconda ucsc-bigbedtobed to install) and then either use a tabix-indexed BED file or convert BED to BAM (bedtools bedtobam program).

Changes in v0.5.5.1

  • change DifferentialExpressionResults.scatter default plotting style to have linewidths > 0. Previously, using linewidths=0 caused plots to show up blank in IPython Notebook on Mac

Changes in v0.5.5

  • add metaseq.tableprinter module

Changes in v0.5.4

  • metaseq.results_table.DESeq2Results class
  • handle cases where callbacks could be called multiple times
  • support marginal histograms of length-1 arrays
  • metaseq.persistence functions use absolute path for features to make symlinking more robust
  • differential expression classes cleaned up and refactored
  • new kwargs for metaseq.plotutils.imshow: figure_kwargs, subset_by, subset_order
  • new metaseq.plotutils.add_labels_to_subsets helper function

Changes in v0.5

v0.5 marks a major improvement and maturation of metaseq but at the expense of backward-compatibility. The changes are too numerous to list, but include massive plotting improvements, speedups, more flexible API, and much more.