args to Local::DB either dsn or dbname; integration with other apps and Local::QueryLogger; switched off query logging for test scripts

simplified args passed in NGS.pm method calls - src_data & data_file are equivalent so replaced all refs to former with latter; simplified config block in _parse()

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

separated hmds_ref into request_number & year for ease of order by on sample data retrieval

frequency calc in save_data() truncated to %2d; file-type changed to .txt as data is tab-delimited so XL can't open it properly as .csv

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

added col headers to csv output

bugfix: dancer_app->environment automatically becomes a config var when defined in Test::Common, otherwise needs manually adding to config (removed from form_opts)

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

added ability to set max x & y-axis values in chartdirector output; 02-vcf-analysis script loads ngs.locations db table for use in start position exclusions

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

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

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