Tags

v2.4.2

v2.4.1

Fix API version

v2.4.0

 - assume LAPACK is always present and use it as a default solver
 - add --sponged-fraction-cutoff and rename --relative-cutoff to --bound-fraction-cutoff
 - use Yan et al. model by default and add a none option to --supplementary-model
 - automatically locate score tables
 - add explicit flags for FASTA flavours

v2.3.0

This release brings a very nice set of features that makes miRBooking
more robust, efficient and convenient to use.

 - add --version flag
 - locate the default score tables automatically
 - fold the seed with a mask and temperature
 - add gene_accession and gene_name to the output format
 - introduce a new tsv-detailed format
 - add support for LAPACK and MKL LAPACK solvers
 - reintroduce SuperLU MT solver
 - select best available solver
 - move I/O facilities in the broker
 - add a blacklist filter system
 - add a new mirbooking-iterative strategy to solve the system gradually
   using the blacklist filter

v2.2.3

Backport various improvements from the 2.3 series:

 - install 1/2/3 mismatch score tables
 - use installed 7mer-3mismatch table by default
 - use installed 3mer (Yan et al.) or 4mer (Wee et al.) by default
 - check for sparse solver availability at runtime
 - fix parsing of gene names from NCBI FASTA
 - remove SuperLU MT codepath that was not intended for 2.2 series
 - add support for OpenBLAS and ATLAS flavours of CBLAS
 - factor kother contribution into Km
 - fix bug in target site vacancy formula

v2.2.2

v2.1.3

v2.2.1

v1.2.5

v2.0.3

Fix CUDA root build issue.

v2.2.0

v2.1.2

 - use 2.1 API version
 - fix usage of 'cuda_root' option

v2.1.1

v2.1.0

 - compute true vacancy using position factorization
 - add API for retrieving various quantities and rates
 - make the broker entirely reproducible from its publicly exposed state
 - use standard masks for seed in generate-score-table
 - rename 4-mer supplementary model to Wee et al. 2012
 - use a struct for representing an interaction score
 - use CBLAS (or MKL CBLAS) in odeint
 - add support for PARDISO solver

v2.0.2

v2.0.1

v2.0.0

v2.0.0-alpha

v1.2.4

 - speedup lookup in 5' direction when computing the vacancy
 - fix missing nucleotide in 3'UTR footprint
 - support GENCODE-style annotations
 - generate a manpage with help2man