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

sorted vcf data by chromosome and start position before writing vep input - same as for 454 data

moved forking config to config files - dev server faster without forks, deployment optimum with fork = 2; moved hires timer to immediately either side of vep script loop; deleted vep input file from /tmp if exists due to generation using append mode (in case previous run aborted before unlink) event; output format tweaks

bugfix: optional lab number prefix needs to be specified as A-Z not \w

added new counters for vep input rows and raw src_file rows; patched lab number regex to allow optional letter prefix; fixed test scripts to report vep input row count instead of 'accepted' rows

sorted vep input file by chromosome using Sort::Naturally - no obvious speed increase

took vep_fields into CONSTANT for use in both 454 data & vcf data; put vcf data into %exon_data_ref for use in post-vep processing (as used in 454 data-files); adapted vep_location / ref_location comparison to handle insertions where end position < start position; moved counts & errors into separate 'data' hashref in results; completed adaptation of VEP for vcf data-files

adapted NGS::VEP to accept vcf files - imported vcf-to-vep.pl script code