extended download function to sample data, split existing vep & non-cds downloads into separate files; moved update_vep_table() function into new save_data() method

moved all db queries to NGS::DB; added download facility for processed data; new MySQL ngs db for download data

new route - app version history; replaced system calls with CPAN Git library; exon links jump directly to selected gene/feature in vep results table

major version change: refactored _run_vep() to select consequence, variation, sift & polyphen values from specified gene/feature combination (multiple entries for same exon_id from vep, with varying sift, polyphen, consequence & variation vals taken into hashref meant last one wins); added cds and protein annotation vals; vep data row skipped & warning issued if ENSG0000* gene id not present in transcripts db

re-arranged order of loaded modules in NGS.pm to avoid redefined var warning; moved vep results from template var to vars var; replace BioSphere::api_version with a Moo 'has' api_version to avoid error in get_cache_types() when called from NGS.pm

restructured NGS _parse() function to use File::Basename; vep results view hides empty tables if no data

fixed broken vcf file upload - now accepts single vcf file, zipped single vcf file & zipped directory of vcf files

new transcripts table for highlighting selected gene/feature combinations

added functions to retrieve and display vep api_version and app version

added myseq.zip to repo; minor presentation tweaks

major upgrade - app uses vep api_version to look for available cache types (ensembl, refseq, merged) and disables any from selection if not available; results page displays api version and selected cache database; vep wrapper captures vep.pl stderr for display on results page; added vcf 'filter' col to results page; enabled HGVS notation function

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

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

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

added transcription db = refseq option; fix for FLT3-ITD 1 variant; tests for invalid variant format