Segtools

* segtools-feature-distance: fix feature distance only counting last chromosome
* segtools-overlap: fix type casting bug

* segtools-aggregation: fix bug: --mode gene option resulted in "ufunc 'rint' output (typecode 'd') could not be coerced to provided output parameter (typecode 'l') according to the casting rule ''same_kind''"
* segtools-aggregation: fix bug described in the Issue 44: Segtools aggregate in gene mode not necessarily pick the longest transcript. (Mickael Mendez)
* replaced deprecated rpy2 calls to "set_writeconsole"
* segtools-signal-distribution: Switched to using "longdouble" precision, in order to provide more accurate mean and variance estimates. (Max Libbrecht)

* add "narrowPeak" as synonym format for "bed"
* segtools-overlap: fix bug where totals above 2**31 could not be
calculated on 32-bit machine
* segtools-signal-distribution: fix bug: --indir option resulted in "can't multiply sequence by non-int of type 'str'" error
* segtools-gmtk-parameters: add R transcripts
* segtools-gmtk-parameters: unescape escaped tracknames from newer versions of Segway
* segtools-relabel: add color support
* add segtools.get_r_dirname() function
* R transcripts: add !/usr/bin/env Rscript at top
* R transcripts now get source files using get_r_dirname()
* move from use of reshape to reshape2
* signal-distribution now gets a transformation as an option and apply it on data (Habil Zare)
* A bug in signal-distribution is fixed that resulted in incorrect labeling. (Habil Zare)
* support for Cairo (http://www.cairographics.org/) has been added for systems with the R Cairo package. Cairo does not require X11. (Jay Hesselberth & Paul Ellenbogen)

* segtools-signal-distribution: cleaned up code and arguments to only support
accurate computation of statistics (and not histogram approximation)
* segtools-signal-distribution: rewrote calculation loop to improve speed
(now takes ~ 2hrs for chr1 with 93 tracks)
* progress bars now include ETA.

* 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.

* __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