CHANGES
=======

0.2.1
-----

* Update readme
* Error in coordiates recomputation fixed
* Tests fixed
* tests for rnftools liftover
* rnftools liftover works
* Minifix
* Minifix
* rnftools liftover adapted to new api
* Fasta index from a chain
* Coordinates liftover partially reimplemented
* View TODOs
* Minifix
* rnftools.utils
* rnftools liftover - make lifting coordinates working
* rnftools liftover
* BAM chain-lifting
* List of position mapping from a chain file, lifting a FASTQ file
* Minifix
* Documentation for rnftools validate
* Refactoring + documentation update
* Synchronizing widths in RNF names when joining FQ files
* Refactoring
* Example with all supported simulators
* rnfformat.RnfProfile
* rnftools validate
* rnf-spec link

0.2.0b0
-------

* Small changes in documentation structure
* How to add a new plugin
* More links in readme
* Better instructions for installation
* Minifix
* Documentation included in the tests
* Examples location update
* doc: main help message from rnftools
* Help for command-line rnftools
* bats configuration experiment
* Fix
* Git in the list of required software
* bats -- pretty output format (for seeing the differences)
* Minifix
* bats installed from a ubuntu repository
* Minifix
* Naming style for files with classes unified
* Tests using bats
* Class for merging moved to rnftools.rnfformat
* Docs: record for DNemulator
* rnftools merge -- messages
* Other tests for rnftools
* Reg. express. in CuReSim doc
* Removing new line characters from CuReSim output
* rnf-join-fq => rnftools merge
* rnftools check
* rnftools sam2roc
* Minifix
* rnftools - lavender subcommands
* lavender refactoring - part 2
* lavender refactoring - part 1
* rnftools publication
* Better help messages for rnftools script
* rnftools curesim2rnf
* Tests for Mason SE/PE, Art PE
* Fix
* Minifix
* Small fix
* Minifix
* command line - support for dwgsim and dwgsim, tests
* rnftools as a command line tool - basic version
* Configuration for the package
* Possible switching intro info off
* Better detection of version
* Minifix
* snakemake.shell => smbl.utils.shell
* Art plugin: remove transformation of SAM (bug in Art corrected)
* Bug in version detection
* Attempt: different Python version for tests
* Recode CuReSim FASTQ to RNF FASTQ as a static method
* WgSim static method bug corrected
* FASTQ to RNF convertion as static method for WgSim - not working yet
* Recode DwgSim FASTQ to RNF as a static method
* Added Gitter badge
* Print version
* Recoding SAM to RNF as a static method
* SAM import improved
* Minifix
* Document missing parameters, add regexp for WgSim to docs
* min required versions of packages
* Documentation enhancement
* Tests improved
* Small improvements
* Documentation improvements
* Better links in documentation, links to source code
* Documentation homepage improvement
* Support for MASON
* Minifix

1.1
---

* Another update of documentation
* Documentation update
* Reorganization of folder with examples of evaluation
* Additional requirements
* New examples - test fix
* Reorganization of introduction
* Rest of simulation tutorials
* Homepage of docs
* Tutorial - examples in standalone files
* RNF format library
* Examples for MIShmash
* Cleaning
* First steps with MIShmash
* Documentation reorganization
* Refactoring
* Few fixes after refactoring
* https for wheels
* Refactoring
* Fix
* Docstrings improvement, refactoring
* Example for PE fixed
* Joining fq files and few other problems fixed
* More parameters for DwgSim
* More parameters for wgsim
* Error in docstrings formatting fixed
* setup.cfg without diacritics
* Ensuring new configparser working correctly with Unicode
* requirements.txt - order of packages changed
* Docstrings in Napoleon style for MIShmash
* Removing old unused message function
* Graphical improvements of graphs produced by LAVEnder
* Adjusting key boxes
* Improvements in reports
* Named colors => code
* Bug in eval. fixed, output improved, examples corrected
* bam-mis-roc => bam-mis-mir-roc
* aci => mis
* HTML output improvement
* T category => T category and t category
* Refactoring
* ACI file possibly compressed
* Searching wheels files directly in web repository
* Travis - pysam from wheels
* ylabels
* Ambiguities dont appear any more
* Parameters for new graphs passed by Report class
* Program header in HTML report
* Adding other graphs - first part
* Try to avoid error in setuptools by its upgrade

0.1.0
-----

* Deployment only for tagged releases
* Fix setup.py
* Fix setup (no need of importing pbr in this file)
* Fix installation script
* PyPI deployment by Travis
* Fix
* Test of PyPI versioning
* Version from GIT
* Install required packages before RnfTools
* Fix
* PySam from a wheel
* Revert "PySam installation from Ubuntu packages" - does not work in Travis version of Ubuntu
* PySam installation from Ubuntu packages
* .gitignore update
* LAVEnder plotting improvement
* Bug with multimapped reads detection
* Travis C++11 fix
* Better example
* Fix of ambiguity in one of examples
* BWA-SW in example 03
* Examples use BWA class from SMBL
* Several fixes
* Permission - fix
* Refactoring, rnfformat subpackage
* Documentation configure file update
* Unused simulators
* Another attempt
* Attempt to include original read format
* Small fix
* Several small corrections
* Few fixes, difference parameter configurable from lavender.Report
* LAVEnder - parameters for plots
* Bug correction
* Many bugs fixed
* Test update
* fix
* Tests for Travis
* travis image
* Adding Introduction to documentation
* Content update
* Version 0.0.2
* Documentation update
* doc strings for other simulators
* Inheritance in doc
* doc strings for CuReSim
* Better doc strings for ART Illumina
* Other publications, doc strings for ART Illumina
* Links to simulators
* ART publication
* RNF section in RNFtools docs
* Big doc update
* readme
* Multiple os tests
* Examples - tests
* FAQ - sw update
* Travis
* Many fixes
* Small fix
* Recursion fix
* Small doc update
* Small doc update
* Information for developers
* Information for developers
* Content fix
* Content fix
* Other few updates
* Other few updates
* Menu fix
* Menu fix
* Requirements for RTFD
* Requirements for RTFD
* Documentation update
* Documentation update
* Doc. structure
* Doc. structure
* Big update of the package
* Integrating lavender and mishmash into a single package
* Add 'lavender/' from commit 'fad8def26f72a1c25f114421d2252d4d35fa31c2'
* Add 'mishmash/' from commit '9e0f22b36e01c46a91d712bfdbf7a7c8f16d392f'
* Initial commit
* Big update -- mixing of fastq files, different output formats for pair-end
* Number of sources check in a sample
* Read suffixed added, CuReSim update, WgSim single-end, many small updates
* Support for WgSim
* .output => .input
* Support for CuReSim
* requirements for building documentation
* requirements for building documentation
* Small gitignore update
* Small gitignore update
* Documentation generating
* Documentation generating
* Link to RTFD
* Link to RTFD
* Small corrections
* Small corrections
* First version of documentation
* First version of documentation
* Small upd
* Var. table, better links
* Few minicorrections
* Update README.md
* Usage
* Lists correction
* Small updates
* Examples added
* Other updates
* Updates
* Documentation
* Documentation setting
* Template for documentation
* Better example
* Better example
* Several small updates, example corrected
* Several small updates, example corrected
* Big update, several bugs corrected, ART output processed by pysam
* RNG fix, pair-end corrected, etc
* Support for more samples
* Better organization of files
* Big update
* First fully working version
* Small HTML file
* First working version, currently without HTML reports
* Reads count bug correction
* Creating a package
* Refactoring
* Update README.md
* Initial commit
* Create README.md
* New repository - maintenance
* Small corrections
* First working version
* ArtIllumina, sam2fq conversion, Mason; does not work, yet
* New advances
* mishmash reorganization
* Today's work
* Using library
* mishmash
