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

moved NGS::Test function to NGS::Test::Common & moved test-lib.pl functions to NGS::Test, removed all calls to test-lib.pl from tests

major rewrite of test scripts - adapted for D2 version .154 - replaced D2::Test with Plack::Test; new NGS::Test Import::Base class

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

bugfix - recent change to locations table didn't take effect; moved _run_vep() %vep_cols to global var %VEP_COLS

added more exclusions to locations db

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

modified _build_vep_input to include vcf file in rename regex so no longer need to skip in unlink files loop if filename eq vep_input

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