Version 0.3.4:

- Off-target bins (antitargets) are now optional, to the extent that empty
  antitarget BED and .cnn files can be used. This feature can be used for
  testing or, if you must, to analyze targeted amplicon sequencing data.

Version 0.3.3:

- Aesthetic improvements to plots
- Fixed an edge case where a very small BAM file could mistakenly appear to be
  unsorted.

Release v0.3.2: fixed automatic annotation of targets

This fixes the "--annotate refFlat.txt" option, available in the "target" and
"batch" commands, which adds gene names to unannotated 3-column BED files.

Release version 0.3.1, featuring new import and export options

- Export segments to THetA2's input format, for quickly inferring tumor purity and subclone structure
- Import THetA2 results back to CNVkit's segment format (.cns)
- Export segments to FreeBayes --cnv-map format

Release v0.3.0:

- Enable "batch" to be run without specifying tumor samples, in order to only
  create a reference
- Copy ratios are now re-centered at the smoothed "mode" (peak density) rather
  than median, for better behavior on samples with many large-scale losses
- Minor fixes and improvements to several safety checks in response to feedback
  from users

Released with the bioRxiv preprint. Compatible with bcbio-nextgen.

Release v0.2.2 for PyPI -- minor bug fixes

Tagged point release 0.2.1 -- revised dependency versions from 0.2

Release version 0.2