changed method of finding sqlite db in NGS::DB from search of @INC to using D2::FileUtils::path(); added functionality to create separate vep inputs per chromosome - not in use

moved forking config to config files - dev server faster without forks, deployment optimum with fork = 2; moved hires timer to immediately either side of vep script loop; deleted vep input file from /tmp if exists due to generation using append mode (in case previous run aborted before unlink) event; output format tweaks

took vep_fields into CONSTANT for use in both 454 data & vcf data; put vcf data into %exon_data_ref for use in post-vep processing (as used in 454 data-files); adapted vep_location / ref_location comparison to handle insertions where end position < start position; moved counts & errors into separate 'data' hashref in results; completed adaptation of VEP for vcf data-files

adapted NGS::VEP to accept vcf files - imported vcf-to-vep.pl script code

moved chart making functions to new ChartMaker class

patched VEP::_get_hmds_refs to return error if col header doesn't look like lab number; 015_data.t to test

added 2 cols to VEP table (position in CDS and position in protein; added 12 new exons in ref table

escaped spaces in tt a name var; changed production env flag to deployment

replaced (most) test data files with data strings; moved common data structure constructs out into test-lib.pl

more tests; dropped :syntax on use Dancer2

added Modern::Perl; row counters on results tables

replaced server port with dancer_app->environment as flag for debugging to file

using server port as flag to dump vep data to debug file; fixed results.tt loading of sift & polyphen cols when not needed

clearing up mess made by copying dev server and push changes

minor edit for synchronisation between dev platforms