bugfix - total count incorrect for linux zip files which include directory - patched to count only io(<file>)->type eq file

patched miseq_vcf() unlink block to skip non-file items - Archive::Extract ->files includes directory as a file for linux .zip

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()

application errors handled by 500.tt template; filename format error handling

added debug function to NGS::DB; increased max col length for exon_ref to 255 chars

trapped dbi errors in try/catch block, so handled same as other VEP.pm errors; replaced NGS::MooX::Types with Local::MooX::Types; changed existing_variation col in vep_data & sample_data tables to TEXT due to entry >255 chars

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

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