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

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

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

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

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

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

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

added log_dir info to deployment config for compliance with recent D2 upgrade; new test of file upload using LWP::Protocol::PSGI as replacement for depracated D2::Test

changed method of finding sqlite db in NGS::DB from search of @INC to using D2::FileUtils::path(); added functionality to create separate vep inputs per chromosome - not in use

removed allele from exon_data_ref sample_data for both 454 and vcf data - not sure if it's needed; removed vaiable data fields from exon_data_ref for vcf files to match 454 data - vf & depth are variable & change between samples, chr, start_position, end_position, etc do not