CHANGES
=======

0.1.0
-----

* Fix Travis config
* Nightly Python builds, deployments only for tagged commits
* Fix address of XS
* Fix setup
* Other ssh=>git conversion
* setup.py fix
* git clone using git protocol
* Fix installation script
* README syntactic correction
* Few small configuration changes
* SW installation before package
* RST table correction
* Pbr installation
* Automatic PyPI deployment
* Automatic PyPI deployment
* Automatic PyPI deployment
* MrsFast can be now compiled in parallel
* Limiting number of cores for testing
* Tests improved, error-proof downloading + compilation
* Travis C++11 fix
* Travis C++11 fix
* Travis C++11 fix
* Travis fix
* Fix
* Better support for testing (verbose output)
* Seqan - orders of commands changed
* Mason=>Seqan, RaserS added (with sup. for mapping), colored outputs messages (cur. state)
* Support for mapping by Bowtie2 single-end
* Better CygWin support
* Test for compatible programs
* Testing without cores
* git svn for travis testing
* Installation using plugins completed
* Many new plugins
* DwgSim installation - new system
* WgSim installation correction
* Installation - new features (OS detection, etc.)
* New methods for installation of programs
* Fix
* Plugin for WgSim
* Revert "Testing with Python 3.5"
* Testing with Python 3.5
* Small corrections
* System for plugin - first working version
* Plugings
* Automatic rules for mappers
* Support for BWA-SW
* Tests - fix
* Class for BWA
* Permissions - fix
* Fix
* Fix - tests
* Fix - list of subpackages
* Repository reorganization, functions for RNF format moved to RNFtools
* Better support for CygWin
* Template for documentation
* Basic example part of testing
* Small update
* Max 12 cores for parallel installation
* travis image
* Picard + few small fixes
* Test improved
* Multiple os tests
* test output description
* PySam not required
* Mason installation method changed
* Executable flag
* Fix
* Test update
* Tests for Travis
* Travis
* Support for pbsim and xs
* Large update:refactoring,bugs corrected,parallel make,std output reduced,better messages
* version updated
* Suffix in read name
* Curesim added, Mason problem corrected, few other bugs corr
* Small update
* RNF -- automatic block sorting
* Small change in some functions
* RNF ___ bug corrected
* Support for GnuPlot4
* Support for GnuPlot5
* Support for the LAST mapper
* Support for the Bowtie2 mapper
* typos
* Support for the mappers sirFAST, drFAST, mrFAST, and mrsFAST
* Support for the PerM mapper
* Support for the FREEC program
* Support for the GEM mapper
* Support for the BFast mapper
* Support for Mason
* Support for the SToRM mapper
* Typo
* Typo, mail
* Documentation update
* Better directory organization, ART bug, HG38
* Small corrections
* Package improvements
* Reflecting the last changes in package distribution
* Support for destringization in the RNF classes
* Installation from PyPI
* Support for library installation
* RNF classes
* A bug in Snakemake corrected, evals work
* Wgsim added
* Typos
* Updated with respect to changes in the library
* File reorganization, rules for fasta
* Example added
* Typo
* Basic info
* Current version
* Initial commit
