1.1.8:
* segtools-nucleotide-transition: significant (several-hundred-fold) speedup
* segtools-transition: added R transcript
* segtools-aggregation: added R transcript
* segtools-overlap: Fixed bug in argument parsing that caused R plotting to fail
* docs: Added high-level structured summary of the output of each command
* requirements: Genomedata package now only required to use segtools-nucleotide-transition and segtools-signal-distribution, not for unrelated commands
* docs: Unified usage terminology to use "annotation" and "feature" (instead of "annotations" and "entries", for example)
* segtools-*: Added -R option to allow command-line specification of R
  options to segtools commands that plot using R.

1.1.7:

* __init__.py: add gzipped pickles
* segtools-overlap: add R transcript
* segtools-overlap: add --max-contrast option
* __init__.py: _from_pickle: fix UnpickleError message
* common.R: fix a comment character-related bug
* common.R: perl-style regexes for trackname translations
* docs: automtically add --help output to every command
* segtools-length-distribution: allows more generic ANNOTATIONS as input
* segtools-length-distribution: added --no-segments and --no-bases
  flags to control display on size summary plot
* segtools-nucleotide-frequency: improved speed by caching 
  whole chromosome sequence
* segtools-relabel: added command to relabel a segmentation
* segtools-feature-distance: added histogram visualization output
* segtools-preprocess: if OUTFILE is specified, the .pkl.gz extension is still added

1.1.6:

* aggregation.R: fixed syntax error that caused segtools-aggregation to crash

1.1.5:

* common.R: print.image: create the filepath's parent directory, if it
  doesn't already exist
* fix bug related to: allow comment character of # in mnemonics files,
  and automatically add a comment to generated mnemonic files
* segtools-gmtk-parameters: fix bug related to: doesn't generate
  hierarchical mnemonics when Segway subseg is used but has
  cardinality 1

1.1.4:

* allow comment character of # in mnemonics files, and automatically
  add a comment to generated mnemonic files
* segtools-html-report: fix some problem with os.path.samefile()
  (maybe related to Python 2.7+)
* segtools-gmtk-parameters: doesn't generate hierarchical mnemonics
  when Segway subseg is used but has cardinality 1
* add requirement of numpy>=1.3 (because histogram semantics change in that version)

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
