Changes in version 1.0.4 (2019-09-16)
+ Fix check that contig to cluster by was found when specified.
+ Added support to plot_cnv for cell groups with exactly 2 cells.
+ Fix which input file type is checked.
+ Made it so that plot_cnv recalculates clustering automatically if non null ref_contig argument is provided.
+ Fix for plot_cnv() when providing multiple ref_contigs and cluster_by_group is False.
+ Fix only 1/n genes being taken into account when using n ref_contig in plot_cnv.
+ Fix error in file creation when using multiple ref_contig and cluster_by_groups=FALSE in plot_cnv.
+ Bayesian filtering now preserves CNV ids in outputs
Changes in version 1.0.3 (2019-07-05)
+ Fix missing dendrograms in text output when drawing figures.
+ Fix path to save object to when splitting references.
+ Fix file name creation when using num_ref_groups option.
+ Fix reference cells indices returned from method that splits references in num_ref_groups when references are not sorted and at the beginning of the matrix.
+ Fix to support of data.frame as input type for counts matrix.
Changes in version 1.0.2 (2019-05-21)
+ Reduce peak memory usage.
+ Fix to subclusters definition when using a sparse matrix and a non random trees method with no references.
Changes in version 1.0.1 (2019-05-20)
+ Improved when the clustering is defined for groups when running in sample mode.
+ Fixed support for NA to be understood as an output_format value to plot_cnv() in case a user only wants to generate the text outputs and not the plot.
+ Fix ordering of cells and color bars on the heatmap and text outputs when cells are not sorted in the same order in the input matrix and the annotation file.
+ Fix to (sub)cluster definition when a group only has 1 cell.
+ Fix plot_cnv() to handle observations groups with only 1 cell (that can't be hierarchically clustered), a single reference group when no references are not clusterd, and a single reference group with a single cell.
Changes in version 1.0.0 (2019-05-02)
+ Released as a BioConductor packages
Changes in version 0.99.8 (2019-04-20)
+ Fix missing labels on heatmap due to change in how axis() handles overlaps.
+ Improve auto thresholding of heatmap colors to still work when using stronger denoise settings.
+ Updated some examples to use tempfile() for output.
+ Fix duplicate piece of code that produced an error when using plot_steps.
Changes in version 0.99.0 (2019-03-15)
+ Submitted to Bioconductor