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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.
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