P3X GitList

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June 2, 2014

Browse Changes

new vcf analysis section; moved ChartMaker to NGS::ChartMaker

afdff6d83b4d456ca173b2481753928d4e7f79cd afdff6d

RAJ authored on 02/06/2014 13:11:11

January 8, 2014

Browse Changes

moved ngs.pl startup script stderr & stdout to go to NGS/logs/deployment.log; made path to debug.txt explicit in NGS::VEP

e205aa8729e159d0a968bb3a9a6ad0ddf64d120b e205aa8

raj authored on 08/01/2014 15:47:35

September 9, 2013

Browse Changes

needed FindBin in app.pl after update to D2 v0.09; bootstrap 3.0.0 spacelabs theme

a5554a847581abd22c232424c987271c31dfe016 a5554a8

raj authored on 09/09/2013 09:44:32

August 12, 2013

Browse Changes

patched VEP::_get_hmds_refs to return error if col header doesn't look like lab number; 015_data.t to test

3e9e2be86757392f11cd444a7d454c40e45458e1 3e9e2be

raj authored on 12/08/2013 10:15:18

August 8, 2013

Browse Changes

fixed refseq selection function - required separate cache dir & use of --dir option

060f9b46756865d4fd73289a1830dfd4e47121eb 060f9b4

raj authored on 08/08/2013 13:31:19

August 7, 2013

Browse Changes

added transcription db = refseq option; fix for FLT3-ITD 1 variant; tests for invalid variant format

fc57a013f0a3a7de76244c4c5787168ce92c2622 fc57a01

raj authored on 07/08/2013 12:50:32

July 24, 2013

Browse Changes

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

675dc2013e25450e81d28d155fc6f9c4a035c284 675dc20

raj authored on 24/07/2013 15:31:53

July 23, 2013

Browse Changes

renamed vep orphans to non-CDS regions; added new ref entry to sqlite db; results page displays input src filename

7679550722c6ae322cbc69c1f159475472ff8269 7679550

raj authored on 23/07/2013 12:08:39

July 19, 2013

Browse Changes

added 2 cols to VEP table (position in CDS and position in protein; added 12 new exons in ref table

fb1780244371ff130751690f9eac378526e0b439 fb17802

raj authored on 19/07/2013 16:31:16

July 1, 2013

Browse Changes

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

8a8dc6058d6bf2168ea00952e47eaa6d799ef2a9 8a8dc60

raj authored on 01/07/2013 17:00:00
Browse Changes

escaped spaces in tt a name var; changed production env flag to deployment

240e2212b5aaf8c0de7beb7830a899de717b1a6d 240e221

raj authored on 01/07/2013 09:51:28

June 28, 2013

Browse Changes

added specific vep row counter to sample_data results for use in both sample match and sample no-match displays

8e4e35cb2e34fdda478bd96510d5e182699dd00e 8e4e35c

raj authored on 28/06/2013 11:49:55

June 26, 2013

Browse Changes

discontinued NGS::MooX::Types; put proper result counters in using VEP result_counter attribute

df9c8bf2c22d81e062fb5af1c4a90a124b031566 df9c8bf

raj authored on 26/06/2013 16:54:04
Browse Changes

changed sample_data to array to allow multiple samples to have same exon variant; changed return algorithm of _want_vep_result()

d7edd730f75071e3fef32399628ed1c142d70036 d7edd73

raj authored on 26/06/2013 15:16:04
Browse Changes

minor VEP variable name changes for clarity

dbb1ae9c871123344aae2acedf79c922c9084eaf dbb1ae9

raj authored on 26/06/2013 12:17:06