CHANGES
=======

1.4.1
-----

* A small fix
* A small fix
* Wget as alternative method of download also for FASTA files
* Use shutil.rmtree instead of bash rm
* If curl NA, use wget
* A small fix
* Wget as alternative method of download also for FASTA files
* Use shutil.rmtree instead of bash rm
* If curl NA, use wget
* A small fix
* Wget as alternative method of download also for FASTA files
* Use shutil.rmtree instead of bash rm
* If curl NA, use wget

1.4
---

* New version of CMake, LAST, Picard, SamBamBa
* git:// => http://
* CuReSim alternative download
* FASTA and BAM indexes for any suffix

1.3
---

* Requirements update
* vcfutils installed together with bcftools
* New GIT repository for MrsFasta
* xs - fix url
* setup.py check
* Print info only in SnakeMake
* Configuration for SMBL package
* Better detection of version
* Other arguments for smbl.utils.shell
* README minifix
* Minifix
* smbl.utils.shell removing consecutive spaces
* Deactivation of Kallisto plugin -- problems with libraries
* PDF in GnuPlot on OSX in devel
* Minifix 2
* Minifix
* Plugin for DeeZ
* Added Gitter badge
* libhdf55 fix
* Print version in the first message
* Minifix
* Add mouse genome to README\ [skip ci]
* Tests: dependencies for Kallisto
* Support for Kallisto, new versions of CMake, Piccard, SamBamba, and LAST
* Big refactoring: utils, single class for a rule, static loading of plugins, test do not delete smbl dir
* Fix - CuReSim_eval
* Typo
* New version of ART
* New version of Picard
* New version of CuReSim
* Chimpanzee genome
* OSX GnuPlot PDF bug fixed
* Exceptions raised by messages, sorting reads produced by Yara
* Name without diacritics
* OSX bug in twobittofa plugin fixed
* PerM OSX bug corrected
* BFast does not work on MacOS
* Minichange
* Minifix - sh scripts
* Better error messages
* Scripts executable from different directory
* macos => osx
* DrFast is not well supported on OSX (OpenMP)
* Minifix
* New installation procedure for PerM - OSX fix
* Function for error messages
* Ambiguity bug -- ambiguous rules are detected and registered only once

0.1.1
-----

* New development status
* New development status
* Messages, platform strings reported
* Fix
* Another fix, only tests on Python 3.5 and 3.4
* Fix
* On Linux dont use use CMake for SToRM
* Single thread Travis test
* CMake plugin
* PyTest for plugins, ambiguities fixed
* PIP and Setuptools upgrade before installation
* Testing FASTA files downloads
* Improve support for download of FASTA files

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
