moved app messaging to Log::Report; validation of vep data before updating db tables; tests scripts test data insert to sqlite in-memory db; switched off console output of vep data structures for devel; trialing optional bootstrap 3.3.6 css

wrapped call to NGS::VEP in try/catch to handle die via 500.tt - works for tests as well; test for invalid filename; display list of valid filenames in upload page

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

replaced server error with error message for unknown file-type; no warnings for 'given' & 'when' if perl 5.18

added functions to retrieve and display vep api_version and app version

minor adjustments

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

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

adapted app for use in apache/plackup/starman environment, using Plack::Middleware::ReverseProxy

recommited previous version due to accidental reversion

changed VEP uri to vep