Initial commit of development branch
Cleaned up PeaksToGenes::Contrast::GenomicRegions and will begin work on PeaksToGenes::Contrast::Stats
Saved status to move development to HPCC
Added files to statistics branch
Modified db/peakstogenes.sql so that a table for the chromosome sizes has been added. Used dbicdump to update the PeaksToGenes::Schema and the result sets PeaksToGenes::Schema::Result::AvailableGenome and PeaksToGenes::Schema::Result::ChromosomeSize. Added a method in PeaksToGenes::Update::UCSC to write the chromosome sizes to file and return to PeaksToGenes::Update both the Array Ref of file strings for the index files, as well as the file string for the chromosome sizes file. Concomitantly, I added a test harness for these functions to t/02-update_ucsc.t.
Fixed SQL and DBIx definitions for the chromosome sizes table.
Added functions and complimentary tests so that the chromosome sizes file will be stored in the PeaksToGenes database and can be referenced by the genome_id in the AvailableGenome table.
Added the PeaksToGenes::Annotate::BedTools::chromosome_sizes subroutine to fetch the chromosome sizes from the user-defined genome using local files defined by the PeaksToGenes::Update module.
Merge branch 'offline' into statistics
Added Wilcoxon testing in the form of a two group Kruskal-Wallis test with normalization for duplicate values. Need to find a better test dataset for t/11-wilcoxon.t, preferably one with less zeros.
Added a subroutine to PeaksToGenes::Contrast::Genes to ensure that the user-defined list of background genes will be unique from the test list of genes
Moved the Wilcoxon test to t/11-wilcoxon
Updated algorithm to make sure the background list of genes is unique. Added threading to the fetching of information from the tables.
Updated threading functions
Added point biserial corraltion function and test harness
Added threaded functionality to PeaksToGenes::Annotate::BedTools
Added threading functionality to the parsing and creation of the insert statment in PeaksToGenes::Annotate::Database
The annotation functions have multi-threaded functionality added to them. Updating a genome takes approximately 30 seconds
Fixed Array Ref of Array Ref error in the parsing of peak annotations
Updated threading