
CHANGELOG FOR VELVETOPTIMISER
=============================

Changes since Version 2.0:

2.0.1:

*	Added Mikael Brandstrom Durling's code to get free_mem and num_cpus for the Mac.
*	Fixed a bug where if no assembly score was calculable the program crashed.  It now sets the assembly score to 0 instead.

2.1.0:

*	Added two stage optimisation functions.  First one is used to optimise for hash value and second to optimise for cov_cutoff.  Both are user definable and default to "n50" for k-mer size and "Lbp" for cov_cutoff.
*	Above necessitated change in command line option letters to minimise confusion.  first stage opt. func is -k for k-mer size and second is -c for cov_cutoff
*	Fixed a bug in Utils.pm where the exp_cov was only calculated for the first two categories and left out the rest.  Now uses all short read categories.
*	Added a command line option -o to pass through extra commands to velvetg (such as long_mult_cutoff etc.)  NB: No sanity checking here!

2.1.1:

*	Fixed a bug where prefixs containing '-' or '.' would cause the script to fail.

2.1.2:

*	Fixed a bug where estExpCov would try and incorporate columns in the stats.txt file that contained "Inf" or "N/A" into the calculation and thereby crash.

2.1.3:

*	Now gives a nice warning when optimisation function returns undef or 0, instead of cryptic perl error message.

2.1.4:

*	Fixed another bug in estExpCov in Utils.pm so it now doesn't count stats with coverage < 2 and contigs of less than 3 * kmer size - 1.

2.1.5:

*	Added support for velveth's new input file types. (bam, sam and raw) and attempted to future proof it..

2.1.6

*	Now prints Velvet calculated insert sizes and standard deviations in assembly summaries, both in the logfile and on screen

2.1.7

*	Takes new velveth help format into account.  Thanks to Alexie Papanicolaou - CSIRO for the patch.

2.1.8

*	Fixed a bug in the Assembly.pm file so it displays the paired end statistics for newer versions of velvet.

2.1.9

*	Added a hash value search step option.
*	Calculates the maximum number of velvet instances to run allowing for the velvet OMP compile num threads.
*	Warns if compiled with velvet is OMP and optimiser threads set to more than number of cpus times OMP threads.

2.2.0

*	You can choose an output folder to put final optimal results into with the -d option.
*	Fixed a potential bug when running as root.
*	Set default 'hashe' parameter to MAXKMERLENGTH that velvet was compiled with.

2.2.1

*	Added an option to manually set a minimum coverage cutoff.

2.2.2

*	Added an option to set the maximum coverage cutoff as a fraction of the expected coverage.

2.2.3

*	Added --version option
*	Added LICENSE
*	Added INSTALL
*	Moved the change log from README to its own file CHANGELOG

2.2.4

*	Fixed a bug when the starting and ending hash values were the same.

2.2.5

*	Re-configured velveth input line checker to handle new velvet options and hopefully future proof it.

2.2.6

*   Changed README to a markdown document. Thanks @andergs!
*   Fixed a findbin issue
*   Uses File::Path remove_tree instead of "rm -r" during cleanup. Thanks for the suggestion @tseemann!
*   Memory estimator can now work with fastq.gz files.
*   Memory estimator failing for -bam and -sam [Torsten]
