1.1.4:



1.1.3:
* segtools-signal-distribution: added --order-tracks and --order-labels options
* install-script: now sets R_HOME enviroment variable which fixes some issues
* docs: fixed dead mnemonic file reference
* bugfix: removed 'new' argument to 'histrogram' for compatibility with
    newer versions of numpy
* bugfix: segtools-html-report no longer crashes when the mnemonic file is
    already in the place where it would be copied
* bugfix: fixed segtools-flatten unpacking error (when --filter option was
    not specified)

1.1.2:

* eliminated exclamation marks
* new autogen stuff from Sphinx to allow man page generation
* Bug fix: segtools-flatten now works when some files specify strand
  information and others don't.
* Install script: now searches for R a little harder, program versions are
  printed when found, and more errors are caught.
* segtools-flatten: added --filter option
* Docs: added workflow flowchart

1.1.1:
* Plotting: No longer plots to screen. This makes plotting cleaner, less
  error-prone, but slightly slower.
* Documentation: Updated to include command syntax

1.1.0:
* Filled in large holes in documentation
* Improved robustness of installation script
* Renamed many of the Segtools commands for simplicity
* Made BED/GFF files interchangable for most arguments
* Added ability to pre-process segmentations with segtools-preprocess
* Made aggregation significance non-default (since it is not yet mathematically sound).
* Cleaned up command-line interfaces
* Sped up aggregation

1.0.0:

* Added additional functionality to feature-distance
* Added flatten-bed module
* Improved g[ft]f handling of comments
* Overlap plot is now in P-R- instead of ROC-space
* Added significance to aggregation plots
* Updated mnemonic file specification

0.1.2:

* Allowed parallelization of signal distribution
* Added overlap heatmaps
* Removed GSC interfacing for overlap significance

0.1.1:

* Improved all plots
* Improved GMTK support
* Improved HTML report and added explanations
* Bugs still exist in signal_distribution
* GMTK still not separated

0.1.0:

* Initial release
