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

substituted Path::Tiny for D2::FileUtils to supply path() method

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