NEWS

CHANGES IN VERSION 1.7.2, 23 January 2016:
    * Fixes bug where extra keyword-arguments passed to simulate_experiment when using a GTF file would cause an error.

CHANGES IN VERSION 1.7.1, 17 November 2015:
    * Now supports writing more than 1 million reads by chunks. Changes implemented by Rory Kirchner and verified by Leonardo Collado-Torres.
CHANGES IN VERSION 1.2.3, 31 March 2015:
    * change URL of example chromosome 22 sequence dataset / do not test internet-connectivity-dependent stuff during check

CHANGES IN VERSION 1.2.2, 9 March 2015:
    * bug fix in fragment start position simulation with positional bias

CHANGES IN VERSION 1.2.1, 14 January 2015:
    * major refactor: 
        - reduced number of arguments for wrapper functions (simulate_experiment and simulate_experiment_countmat)
        - shortened source code in wrapper functions by adding several internal helper functions 
    * several new features added:
        - GC bias in expression
        - empirical fragment length distribution model available
        - positional bias in fragmentation step
        - empirical error models available
        - custom library size factors available
        - simulate_experiment_empirical function added as quick way to simulate an experiment with abundances derived from a data set

CHANGES IN VERSION 1.99.3, 5 December 2014:
    * NB function now exported
    * note that version 1.99.3 on GitHub was version 1.1.0 on Bioconductor.

CHANGES IN VERSION 1.99.2, 16 November 2014:
    * bug fix in fragment generation (last 2 bases of transcript were never sequenced)

CHANGES IN VERSION 1.99.0; tiny fixes in version 1.99.1.

Version 0.99.1 became release version 1.0.0.

CHANGES IN VERSION 0.99.1, 22 September 2014:
    * fixed bug where read names were incorrect in output fasta files
    * updated vignette
    * added biocViews
    * fixed coding style

Package submission, version 0.99.0, 18 July 2014