sorted vcf data by chromosome and start position before writing vep input - same as for 454 data

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

bugfix: optional lab number prefix needs to be specified as A-Z not \w

added new counters for vep input rows and raw src_file rows; patched lab number regex to allow optional letter prefix; fixed test scripts to report vep input row count instead of 'accepted' rows

sorted vep input file by chromosome using Sort::Naturally - no obvious speed increase

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

vcf-to-vep edits for clarity

tidied & simplified vcf-to-vep script; replaced split & join @bases with a substr function

new vcf-to-vep.pl script; adapted NGS::DB to find sqlite db from t/ and scripts/vcf

added runID col and total number of variants count to tables; removed duplicate genes in GI entry

bugfix to regex - was greedy matching capturing FC string; css & template tweaks

new vcf analysis section; moved ChartMaker to NGS::ChartMaker

converted ChartDirector to Moo class

moved chart making functions to new ChartMaker class