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  • 459b3fe (HEAD -> master) 22/01/2018 13:13:56 by RAJ   update 014_data.t to match previous change in VEP error msg * document Log::Report issue with D1 & D2 version
  • 751d964 08/01/2018 14:21:28 by RAJ   increase MAX_REQNUM_SIZE consistent with change to request_number col SIGNED -> UNSIGNED
  • 13de467 27/01/2016 13:25:05 by RAJ   moved app messaging to Log::Report; validation of vep data before updating db tables; tests scripts test data insert to sqlite in-memory db; switched off console output of vep data structures for devel; trialing optional bootstrap 3.3.6 css
  • a7795c0 25/01/2016 14:29:37 by RAJ   added lab number validation before attempting to save data
  • 2b5e5f5 14/12/2015 13:55:56 by RAJ   bugfix - total count incorrect for linux zip files which include directory - patched to count only io(<file>)->type eq file
  • 04e9c0c 07/10/2015 09:54:25 by RAJ   patched miseq_vcf() unlink block to skip non-file items - Archive::Extract ->files includes directory as a file for linux .zip
  • 06e3196 05/10/2015 15:04:39 by RAJ   new script to populate locations.sqlite table; new locations data
  • a4e37ff 02/09/2015 16:09:00 by RAJ   file download returns text/plain mime-type since send_file() seems to be broken for filehandles after D2 update to 0.161
  • c2c02fc 31/08/2015 11:11:49 by RAJ   args to Local::DB either dsn or dbname; integration with other apps and Local::QueryLogger; switched off query logging for test scripts
  • 55dffd7 24/08/2015 13:36:47 by RAJ   removed 31022441 entry from locations table
  • 368e6ce 17/08/2015 11:29:28 by RAJ   switched off auto-inflate dates in Local::DB pending removal of dates -> datetimes in app/templates
  • 59e606b 05/06/2015 09:10:05 by RAJ   increased max lengthg of sample_data.cds to 255 chars; amended recent transcripts gene feature entry
  • e3f9a11 01/06/2015 11:17:34 by RAJ   increased length of sample_data.protein col; new transcripts table entry
  • 3e99361 13/05/2015 13:00:07 by RAJ   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()
  • 1f10da0 12/05/2015 19:20:50 by RAJ   wrapped call to NGS::VEP in try/catch to handle die via 500.tt - works for tests as well; test for invalid filename; display list of valid filenames in upload page
  • 963711f 11/05/2015 16:06:43 by RAJ   application errors handled by 500.tt template; filename format error handling
  • 443545f 11/05/2015 09:45:50 by RAJ   increased maxlength of cds cols to 50 chars; new transcript gene entry
  • d28e5fd 11/03/2015 10:48:42 by RAJ   added debug function to NGS::DB; increased max col length for exon_ref to 255 chars
  • 579814b 04/03/2015 14:37:10 by RAJ   added lymphoid entries to transcripts db; fixed sample_data.consequence col inconsistency with vep_data.consequence
  • 50274f1 23/02/2015 15:59:06 by RAJ   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
  • 39bca29 02/02/2015 15:42:21 by RAJ   separated hmds_ref into request_number & year for ease of order by on sample data retrieval
  • 4137f78 21/01/2015 11:03:12 by RAJ   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
  • e11115f 20/01/2015 18:31:46 by RAJ   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
  • 3db3de6 10/12/2014 14:43:04 by RAJ   added col headers to csv output
  • 86733fd 08/12/2014 15:17:02 by RAJ   bugfix: dancer_app->environment automatically becomes a config var when defined in Test::Common, otherwise needs manually adding to config (removed from form_opts)
  • 7362fb1 08/12/2014 14:30:24 by RAJ   new tests files for scripts
  • d124b47 08/12/2014 14:24:17 by RAJ   moved all db queries to NGS::DB; added download facility for processed data; new MySQL ngs db for download data
  • e2d76aa 28/11/2014 13:07:09 by RAJ   moved NGS::Test function to NGS::Test::Common & moved test-lib.pl functions to NGS::Test, removed all calls to test-lib.pl from tests
  • 66177c5 27/11/2014 23:40:11 by RAJ   major rewrite of test scripts - adapted for D2 version .154 - replaced D2::Test with Plack::Test; new NGS::Test Import::Base class
  • fb8cf50 05/11/2014 17:30:28 by RAJ   added ability to set max x & y-axis values in chartdirector output; 02-vcf-analysis script loads ngs.locations db table for use in start position exclusions
  • 3455a39 01/11/2014 12:14:18 by RAJ   new route - app version history; replaced system calls with CPAN Git library; exon links jump directly to selected gene/feature in vep results table
  • 89412bb 31/10/2014 16:34:59 by RAJ   bugfix - recent change to locations table didn't take effect; moved _run_vep() %vep_cols to global var %VEP_COLS
  • 5475e33 31/10/2014 15:39:07 by RAJ   added more exclusions to locations db
  • d49aa27 31/10/2014 15:18:53 by RAJ   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
  • 0ecf343 06/10/2014 15:01:41 by RAJ   replaced server error with error message for unknown file-type; no warnings for 'given' & 'when' if perl 5.18
  • 1da1fe4 22/09/2014 16:51:32 by RAJ   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
  • 5c6f279 22/09/2014 10:45:09 by RAJ   restructured NGS _parse() function to use File::Basename; vep results view hides empty tables if no data
  • 5c5362e 19/09/2014 16:59:19 by RAJ   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
  • 8f36e33 19/09/2014 16:27:47 by RAJ   fixed broken vcf file upload - now accepts single vcf file, zipped single vcf file & zipped directory of vcf files
  • aa4b5e2 19/09/2014 14:46:08 by RAJ   new transcripts table for highlighting selected gene/feature combinations
  • d3ca976 19/09/2014 11:35:28 by RAJ   added functions to retrieve and display vep api_version and app version
  • 32f4e5a 18/09/2014 16:38:02 by RAJ   minor adjustments
  • 2ae413f 18/09/2014 16:29:12 by RAJ   added myseq.zip to repo; minor presentation tweaks
  • eeb4cd5 18/09/2014 14:27:54 by RAJ   updated test scripts to work with previous app upgrade (eg tests merged db)
  • b307809 18/09/2014 12:41:59 by RAJ   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
  • eee0c21 15/09/2014 10:38:17 by RAJ   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
  • 5dc5589 13/08/2014 23:20:14 by RAJ   Merge branch 'master' of 109.74.205.101:/home/raj/git/ngs
  • 58de245 13/08/2014 23:19:50 by RAJ   replaced Dancer2::FileUtils with Path::Tiny for path() method
  • cf0c0b8 02/08/2014 14:14:00 by RAJ   substituted Path::Tiny for D2::FileUtils to supply path() method
  • dc2b3d9 01/08/2014 11:51:24 by RAJ   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
  • 6b87e4e 09/07/2014 15:44:58 by RAJ   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
  • 52da4ab 09/07/2014 13:27:31 by RAJ   sorted vcf data by chromosome and start position before writing vep input - same as for 454 data
  • de2b317 09/07/2014 12:51:22 by RAJ   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
  • 070e175 09/07/2014 09:32:12 by RAJ   bugfix: optional lab number prefix needs to be specified as A-Z not \w
  • f4b279b 08/07/2014 19:41:56 by RAJ   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
  • 7f76d8e 07/07/2014 15:43:54 by RAJ   sorted vep input file by chromosome using Sort::Naturally - no obvious speed increase
  • 96df262 07/07/2014 14:46:56 by RAJ   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
  • bfd66a5 20/06/2014 15:34:16 by RAJ   adapted NGS::VEP to accept vcf files - imported vcf-to-vep.pl script code
  • 9249628 17/06/2014 15:32:00 by RAJ   vcf-to-vep edits for clarity
  • 99ad964 17/06/2014 14:06:16 by RAJ   tidied & simplified vcf-to-vep script; replaced split & join @bases with a substr function
  • c86edca 17/06/2014 08:27:24 by RAJ   new vcf-to-vep.pl script; adapted NGS::DB to find sqlite db from t/ and scripts/vcf
  • ea26ef0 04/06/2014 14:04:05 by RAJ   added runID col and total number of variants count to tables; removed duplicate genes in GI entry
  • c35b00f 03/06/2014 22:31:19 by RAJ   bugfix to regex - was greedy matching capturing FC string; css & template tweaks
  • afdff6d 02/06/2014 13:11:11 by RAJ   new vcf analysis section; moved ChartMaker to NGS::ChartMaker
  • c6a8493 11/05/2014 13:01:38 by RAJ   converted ChartDirector to Moo class
  • 4489662 11/05/2014 10:39:12 by RAJ   moved chart making functions to new ChartMaker class
  • c56dad5 09/05/2014 16:58:56 by RAJ   new vcf analysis script
  • f3e7ed3 08/01/2014 16:32:27 by raj   updated module_build.pl
  • e205aa8 08/01/2014 15:47:35 by raj   moved ngs.pl startup script stderr & stdout to go to NGS/logs/deployment.log; made path to debug.txt explicit in NGS::VEP
  • 988cd9f 06/12/2013 16:08:08 by raj   updated README's
  • 30e615c 06/12/2013 15:29:02 by raj   changed script/variant_effect_predictor.pl file to symlink to same file inside variant_effect_predictor dir for ease of updating vep version - now just download, extract & run new v_e_p.tar.gz
  • dfac6c4 06/12/2013 13:57:10 by raj   fixed error in previous commit
  • 103891e 06/12/2013 13:51:02 by raj   decoupled NGS::DB from LIMS - moved DBI handling to Local::DB; added module_build.pl
  • a5554a8 09/09/2013 09:44:32 by raj   needed FindBin in app.pl after update to D2 v0.09; bootstrap 3.0.0 spacelabs theme
  • 1894b9e 12/08/2013 12:53:43 by raj   skipped 002_data.t test for 404 error unless D2 versrion > 0.04 - didn't handle 404 error properly
  • 3e9e2be 12/08/2013 10:15:18 by raj   patched VEP::_get_hmds_refs to return error if col header doesn't look like lab number; 015_data.t to test
  • 060f9b4 08/08/2013 13:31:19 by raj   fixed refseq selection function - required separate cache dir & use of --dir option
  • fc57a01 07/08/2013 12:50:32 by raj   added transcription db = refseq option; fix for FLT3-ITD 1 variant; tests for invalid variant format
  • bb7a751 24/07/2013 15:56:52 by raj   added bootswatch spacelab css; added bootstrap table styles
  • 675dc20 24/07/2013 15:31:53 by raj   added errors & alerts display to results output; checks all exon names in src data are in vep input data; updated test scripts with results output format
  • 7679550 23/07/2013 12:08:39 by raj   renamed vep orphans to non-CDS regions; added new ref entry to sqlite db; results page displays input src filename
  • 5c01f95 19/07/2013 17:06:57 by raj   updated ref table (forgot to save changes in previous version)
  • fb17802 19/07/2013 16:31:16 by raj   added 2 cols to VEP table (position in CDS and position in protein; added 12 new exons in ref table
  • 8a8dc60 01/07/2013 17:00:00 by raj   bugfix to _prediction_and_score() - needed to skip undef vars; colour-coded results if deleterious or damaging; truncated long (>30 char) variation results; re-ordered results cols for clarity
  • 240e221 01/07/2013 09:51:28 by raj   escaped spaces in tt a name var; changed production env flag to deployment
  • 8e4e35c 28/06/2013 11:49:55 by raj   added specific vep row counter to sample_data results for use in both sample match and sample no-match displays
  • df9c8bf 26/06/2013 16:54:04 by raj   discontinued NGS::MooX::Types; put proper result counters in using VEP result_counter attribute
  • 5c9a371 26/06/2013 15:18:36 by raj   added new tests
  • d7edd73 26/06/2013 15:16:04 by raj   changed sample_data to array to allow multiple samples to have same exon variant; changed return algorithm of _want_vep_result()
  • dbb1ae9 26/06/2013 12:17:06 by raj   minor VEP variable name changes for clarity
  • 2ca7e17 26/06/2013 11:37:10 by raj   NGS::VEP refactor - changed exon identifier to accomodate multiple point mutations at same locus; all tests pass
  • 30973b5 24/06/2013 17:04:18 by raj   replaced (most) test data files with data strings; moved common data structure constructs out into test-lib.pl
  • 2e4f311 20/06/2013 18:47:47 by raj   more tests; dropped :syntax on use Dancer2
  • a19c503 20/06/2013 17:10:33 by raj   added test suite for VEP data
  • 4f335c3 17/06/2013 09:16:57 by raj   added Modern::Perl; row counters on results tables
  • c3416b2 10/06/2013 16:59:26 by raj   replaced server port with dancer_app->environment as flag for debugging to file
  • 8ec1e37 10/06/2013 16:26:28 by raj   using server port as flag to dump vep data to debug file; fixed results.tt loading of sift & polyphen cols when not needed
  • 2856515 10/06/2013 11:00:26 by raj   replaced / readline with IO::All methods pipe and getline; always returned defined content for sift & polyphen in _prediction_and_score() to avoid empty cells in results.tt; bugfix ngs.css
  • 1b2c3b6 10/06/2013 09:51:41 by raj   clearing up mess made by copying dev server and push changes
  • 856b545 10/06/2013 09:25:08 by raj   minor edit for synchronisation between dev platforms