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

minor adjustments

added myseq.zip to repo; minor presentation tweaks

updated test scripts to work with previous app upgrade (eg tests merged db)

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

Merge branch 'master' of 109.74.205.101:/home/raj/git/ngs

replaced Dancer2::FileUtils with Path::Tiny for path() method