|
bin
|
|
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
|
11 years ago
|
|
environments
|
|
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
|
11 years ago
|
|
lib
|
|
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
|
11 years ago
|
|
public
|
|
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
|
11 years ago
|
|
script
|
|
added functions to retrieve and display vep api_version and app version
|
11 years ago
|
|
t
|
|
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
|
11 years ago
|
|
views
|
|
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
|
11 years ago
|
|
.gitignore
|
492B
|
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
|
11 years ago
|
|
README.txt
|
2kB
|
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
|
11 years ago
|
|
config.yml
|
917B
|
adapted NGS::VEP to accept vcf files - imported vcf-to-vep.pl script code
|
11 years ago
|
|
module_build.pl
|
438B
|
updated module_build.pl
|
12 years ago
|
|
ngs.sqlite
|
52kB
|
new transcripts table for highlighting selected gene/feature combinations
|
11 years ago
|
