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Commits on May 08, 2015
@sajp sajp add return to method 5a20569
@sajp sajp perlcritic fix 063b515
@sajp sajp fix tests for crispr off targets resultset 67a6cc6
@sajp sajp add exhaustive option to off target algorithm when searching for cris…
…prs, fix tests for this as well
Commits on May 09, 2015
@sajp sajp Merge branch 'master' into devel 92f91a1
@sajp sajp v0.313
   Re-work crispr off targets table, these are now links between crisprs.
   - crispr may have many off target crisprs, a mismatch score is also stored
   - updated display of crispr off targets on crispr view page
   - added REST API method to allow crispr off targets to be created
   Added a wide-screen toggle button, state is saved for a session.
Commits on May 11, 2015
@sajp sajp bugfix, if crispr es qc has not yet finshed viewing run threw error b…
…ecause no wells
@sajp sajp add original crispr data to crispr off target table in crispr view 4433413
@af11-sanger af11-sanger fixed bug caused by checkout of last well on plate e6d23ba
@af11-sanger af11-sanger crispr search page: work in progress 09e24a6
@af11-sanger af11-sanger Merge branch 'devel' of into devel 1d393ef
@af11-sanger af11-sanger create_barcoded_plate_copy deemed too complex by perlcritic 0b2f7c5
@sajp sajp add API to retrieve crispr off targets 0f063c8
@sajp sajp Merge branch 'devel' of into devel b2e3d39
@af11-sanger af11-sanger v0.314
    Added REST API to get crispr off-targets
    Bugfix: can now checkout last barcode from a plate
@af11-sanger af11-sanger fixed bug in genotyping_info. then fixed consequences of fixing bug a…
…s QC might be at PIQ or EP_PICK stage
@af11-sanger af11-sanger Merge branch 'devel' aedbafa
@af11-sanger af11-sanger v0.315
   Bugfix: public clone genotyping page now shows ancestor PIQ or EP_PICK QC
Commits on May 12, 2015
@af11-sanger af11-sanger fixed bug in parsing of barcode files with empty lines 1f09a53
@af11-sanger af11-sanger added crispr search by ID page c5e63bf
@af11-sanger af11-sanger on QC summary display pass as boolean string 1f17a1e
@dparrysmith dparrysmith Added 'lims2 psql' command - opens psql using the currently selected
@dparrysmith dparrysmith Updated help to include 'lims2 psql' 6b9b7c3
Commits on May 13, 2015
@tg6 tg6 allow change species on landing page f3cd720
@af11-sanger af11-sanger improvements to clone genotyping info search interface d3a8bcc
@af11-sanger af11-sanger changes to section names in gene summary report e0a6272
@af11-sanger af11-sanger Merge branch 'devel' of into devel f23e7e3
Commits on May 14, 2015
@af11-sanger af11-sanger provide barcode upload option for virtual plates b9773d8
@af11-sanger af11-sanger Merge branch 'devel' a22737c
@af11-sanger af11-sanger v0.316
   Added crispr search page
   Improved clone genotyping search page
   Changed section names in gene summary page
@dparrysmith dparrysmith Added new qc_element_type
Using PostgreSQL CREATE TYPE to constrain the labels allowed
Commits on May 15, 2015
@tg6 tg6 Added append types for CRISPR plates f354650
@tg6 tg6 Merge branch 'devel' of into devel 8efb86c
@tg6 tg6 Merge branch 'devel' ebce55e
@dparrysmith dparrysmith revised schema version 237c606
@tg6 tg6 v0.317
    Added append types for CRISPR plates
@dparrysmith dparrysmith Merge branch 'devel' into david_misc ffc6281
@tg6 tg6 Allow to delete CRISPR plates by removing the appens also d98d89c
Commits on May 18, 2015
@sajp sajp Merge branch 'master' into devel ac60949
@dparrysmith dparrysmith Merge branch 'devel' into david_misc e3120d5
@dparrysmith dparrysmith Updated ddl to use CREATE TYPE for assembly_well_qc_type b35e3f7
@tg6 tg6 Summary schema file fix b0d5b4b
@dparrysmith dparrysmith Changes to add audit and schema regeneration to lims2_setup 2194f7e
@dparrysmith dparrysmith Merge branch 'devel' into david_misc 9da753b
@dparrysmith dparrysmith Updated schema files a9e2b2b
Commits on May 19, 2015
@sajp sajp add update_crispr_validation_status method f56cc77
@sajp sajp add new validated column to crisprs table 4246098
@sajp sajp add REST API method to update crispr validation status 8a9de52
@sajp sajp update format_well_data method in CrisprEsQcWell class to return list of
ranked crisprs, going from left to right.
Also return more information when we have no reads or alignments
@sajp sajp add validated / no validated badge to crispr page 4c1bb08
@sajp sajp add javascript to crispr es qc run page to update a crisprs validated…
… status through REST API

In addition mark all crisprs with the same id with the same status
@sajp sajp add template that displays the crispr validation interface beneath th…
…e alignment section of the crispr es qc page
@sajp sajp only show crispr validation on the main crispr es qc run page efb81a2
@sajp sajp Merge branch 'devel' into crispr_validation ed114c2
@sajp sajp add validated field to crispr resultset test 17f9f47
Commits on May 20, 2015
@tg6 tg6 Added Call on Primary and Distribution QC in gene summaty page 460c887
@sajp sajp make sure format_alignment_strings and ranked_crisprs method return a…
…ppropriate values when we have no crisprs
@af11-sanger af11-sanger mutation signatures additions 2ea7543
@af11-sanger af11-sanger added user view of mutation signatures barcode list b685c7e
Commits on May 21, 2015
@dparrysmith dparrysmith Added actual database name to confirmation message as well as database
@af11-sanger af11-sanger fixed error in plate list query aaaae03
@af11-sanger af11-sanger added interface to look up friendly names in CGAP. Gets url from new …
…config file at LIMS2_URL_CONFIG
@af11-sanger af11-sanger merged latest changes from af11_misc branch c212620
@af11-sanger af11-sanger add new page to navigation menu a405711
@af11-sanger af11-sanger ignore perlcritic no return warning 008d76d
@af11-sanger af11-sanger v0.318
    Added well assembly QC support
    Added mutation signatures barcode list
    Added CGAP friendly name lookup page
Commits on May 22, 2015
@sajp sajp Add crispr_validation table, remove validated flag from crisprs table 3160dc7
@sajp sajp add audit table for crispr_validation 551b703
@sajp sajp add as_hash method to CrisprValidation resultset ecb5a21
@sajp sajp add unique constraint on crispr_id and crispr_es_qc_well_id to crispr…
…_validation table
@sajp sajp move API code from Crispr to CrisprQc 17b52ea
@sajp sajp only show crispr validation interface for qc done on EP_PICK plates b2d4b2b
@sajp sajp get crispr_validation data from new table 8296b7e
@sajp sajp Update crispr validation interface to interact with new crispr_valid…
…ation table
@sajp sajp store list of single crispr ids linked to the crispr_es_qc_well if it…
…s on a EP_PICK plate, this will be used to populate the crispr_validation table with records
@sajp sajp pass a optional list of crisprs_to_validate when creating a crispr_es…
…_qc_well, use these ids to create new crispr_validation records linking the crispr_es_qc_wells with their crisprs
@sajp sajp remove validated column from Crisprs resultset data test 39a5486
@sajp sajp Merge branch 'devel' into crispr_validation fdb6d4f
Commits on May 26, 2015
@sajp sajp Merge branch 'crispr_validation' into devel 7cce44d
@sajp sajp remove validated flag from crispr view 87e4f72
@sajp sajp v0.319
    Add crispr validation framework and interface.
@sajp sajp bugfix, ranked_crisprs method on crispr group returns a array ref, no…
…t a list
@af11-sanger af11-sanger allow discard of barcode during doubling. redirect to scan barcode pa…
…ge instead of barcode lists
@af11-sanger af11-sanger Merge branch 'master' of b3a509d
@sajp sajp show is_rejected info for design genotyping primers 069a435
@sajp sajp fix typo 556ef66
@af11-sanger af11-sanger Merge branch 'master' into devel 8d52dfe
@sajp sajp align rejected badge correctly be85d0b
@sajp sajp Merge branch 'devel' of into devel b6306b5
@tg6 tg6 rejected priver validation flag display updated in design view 36ce143
Commits on May 27, 2015
@sajp sajp bugfix, return link if we have a catalyst object f46e2f6
@tg6 tg6 Merge branch 'devel' of into devel 755a3ff
@dparrysmith dparrysmith Merge branch 'devel' into david_misc 8a71351
@sajp sajp set option for crispr damage type of undef f7819e3
@sajp sajp if no reads then crispr damage type set to no-call ebf0fcf
Commits on May 28, 2015
@af11-sanger af11-sanger fixed bug in generation and display of eng_seq_params when recombinas…
…e is specified for qc_template
Commits on Jun 01, 2015
@af11-sanger af11-sanger removed All checkbox from project sponsor list. It is now selected au…
@dparrysmith dparrysmith David's last commit 3835032
@dparrysmith dparrysmith Merge branch 'devel' into david_misc faa367a
@af11-sanger af11-sanger v0.320
   Barcode can be discarded during doubling
   "All" sponsor selected automatically
@af11-sanger af11-sanger fixed locked row height bug seen in extjs grid in chrome 4afb875
@af11-sanger af11-sanger Merge branch 'devel' into assembly_qc 9c0cfe3
Commits on Jun 03, 2015
@af11-sanger af11-sanger combo boxes now rendered in extjs grid and simple table for reports 95307c7
@af11-sanger af11-sanger assembly qc combo boxes now working d7b6b8c
Commits on Jun 04, 2015
@af11-sanger af11-sanger final tests and fixes to assembly qc combo boxes 5d98203
@af11-sanger af11-sanger Merge branch 'devel' 8e65390
@af11-sanger af11-sanger v0.321
   Added assembly well qc dropdowns to plate reports
Commits on Jun 05, 2015
@tg6 tg6 Added Het checkboxes in crispr_es_qc c00807d
@tg6 tg6 Merge branch 'devel' of into devel 1f1f8df
@tg6 tg6 Merge branch 'devel' into tg6_het c202ada
Commits on Jun 08, 2015
@tg6 tg6 well_het_status now updates well_accepted_override c20a260
@tg6 tg6 Added description to methods dad21ea
Commits on Jun 09, 2015
@tg6 tg6 Merge branch 'devel' 16ff3d4
@tg6 tg6 v0.322
   Added Het validation status framework and interface
@af11-sanger af11-sanger initial work on new EP summary report ae2cc3e
@af11-sanger af11-sanger added no insert to list of assembly qc values e7b7cf5
@tg6 tg6 front page cache params cleaned 48d68aa
@tg6 tg6 Merge branch 'devel' of into devel f092024
Commits on Jun 11, 2015
@af11-sanger af11-sanger completed more columns in report f0163be
@af11-sanger af11-sanger fixed bug which caused extjs grid fail 252a2eb
@tg6 tg6 Added validation and error message at pcr_status_upload 242ef7e
Commits on Jun 15, 2015
@tg6 tg6 Fixed wge_design_importer 7fbe3f1
Commits on Jun 16, 2015
@tg6 tg6 Added no-call count to sponsor sub-report, preparing for het reporting 940e917
@tg6 tg6 no more duplicated crispr groups 2cb61c4
@tg6 tg6 Merge branch 'devel' d910fde
@tg6 tg6 v0.323
   wge crispr importer fix. duplicated crispr group prohibited.
Commits on Jun 18, 2015
@af11-sanger af11-sanger Merge branch 'devel' into crispr_ep_summary bddc99e
@af11-sanger af11-sanger added more data cf76653
@tg6 tg6 fix at sponsor_sub_report 86099ef
@tg6 tg6 Added het clones to sponsor_sub_report ee01ec0
@tg6 tg6 Merge branch 'devel' 45cc94e
@tg6 tg6 v0.324
   Added het clones to sponsor_sub_report
@af11-sanger af11-sanger crispr EP summary report now working. may need some speeding up. 73b0311
@tg6 tg6 removed unnecessary line d64750b
@tg6 tg6 minor fix sponsor sub report e55dd7d
@tg6 tg6 fixed mouse non-crispr sponsor_sub_report 5215db8
Commits on Jun 19, 2015
@tg6 tg6 sponsor sub report het count fix f73ecef
@tg6 tg6 Merge branch 'master' into devel a6561de
@tg6 tg6 create_crispr now updates crispr_loci_type_id if crispr already exists 0b40464
@tg6 tg6 v0.325
   Fixed bug in crispr_loci_type_id of create_crispr
   Fixed bug in mouse non-crispr project sponsor sub report
Commits on Jun 22, 2015
@af11-sanger af11-sanger attempt to improve performance 0ce4c8f
@af11-sanger af11-sanger change status of FP barcodes when creating PIQ plate (Mouse only) 8e56795
Commits on Jun 23, 2015
@af11-sanger af11-sanger fixed report fail caused by missing allele_symbol in imits b552868
@af11-sanger af11-sanger Merge branch 'devel' into crispr_ep_summary f9e3bff
@af11-sanger af11-sanger factored crispr damage type picking out of reports and into util modu…
…le. used in new crispr EP summary
@af11-sanger af11-sanger het calling factored out of sponsor report and used in new crispr ep …
…summary report
@af11-sanger af11-sanger added new crispr EP report to menus 5284d34
@af11-sanger af11-sanger fixes highlighted by tests aaf2a12
@af11-sanger af11-sanger Merge branch 'devel' f6d69f5
@af11-sanger af11-sanger v0.326
   Added new human CRISPR EP summary report
   Mouse PIQ plate creation handles barcodes on parent FP wells
Commits on Jun 24, 2015
@af11-sanger af11-sanger display zeros for damage type counts in human crispr EP summary 48063e8
@af11-sanger af11-sanger bugfix - recovery comment was set to text "null" when empty 9eb4572
@tg6 tg6 sponsor sub report early stage project failure highlighted 10b0494
@tg6 tg6 Merge branch 'devel' of into devel 5015008
@af11-sanger af11-sanger show experiments on gene summary page 8a2d529
Commits on Jun 25, 2015
@af11-sanger af11-sanger Merge branch 'devel' of into devel d267abf
@af11-sanger af11-sanger return HGNC gene ids in es qc well data d576805
Commits on Jun 26, 2015
@tg6 tg6 resized crispr validation/pcr done size 5239662
@tg6 tg6 added fallback in when no accept status is available 639ac53
@tg6 tg6 Added new variant calls: splice_acceptor, splice_donor, intron 19de5a7
Commits on Jun 29, 2015
@tg6 tg6 commented out warnings on crispr_damage_type_for_ep_pick. too slow wi…
…th them
@tg6 tg6 Merge branch 'devel' of into devel 7f80116
@af11-sanger af11-sanger added generate primers button to crispr view 593ab38
@tg6 tg6 Merge branch 'devel' 89301a9
@tg6 tg6 v0.327
    Added new variant calls: splice_acceptor, splice_donor, intron
Commits on Jun 30, 2015
@af11-sanger af11-sanger added assembly well to EP well info and added design and crispr links 8f5c61d
Commits on Jul 01, 2015
@tg6 tg6 cleanup sponsor_sub_report 0e7255f
@af11-sanger af11-sanger refactored primer generation in crispr controller for use with groups…
… and pairs
@af11-sanger af11-sanger Merge branch 'devel' of into devel f00d409
Commits on Jul 02, 2015
@af11-sanger af11-sanger tiny bit of refactoring f4bc693
@af11-sanger af11-sanger fixed test broken by change to gene summary report d298453
Commits on Jul 17, 2015
@PeterFCKeen PeterFCKeen Added view experiment page. Linking off the view project page. 4180709
@PeterFCKeen PeterFCKeen Corrected PerlCritic issues. 585e060
Commits on Jul 21, 2015
@PeterFCKeen PeterFCKeen Final commit on the view experiment interface with tests.
 Added to the test script to include the view experiment page.
@PeterFCKeen PeterFCKeen Merge branch 'master' into devel 970e3f7
@PeterFCKeen PeterFCKeen v0.328
    Added view experiment interface
Commits on Jul 22, 2015
@tg6 tg6 Sponsor front page sub-report updated
Added splice_acceptor calls to the frameshift counts, het clones make a green project, failed project always turn red at the most recent checkpoint
@tg6 tg6 Merge branch 'master' into devel 3fb1f10
@tg6 tg6 v0.329
    Sponsor front page sub-report updated:
    - Added splice_acceptor calls to the frameshift counts
    - het clones make a green project checkpoint
    - failed project always turn red most recent checkpoint
@af11-sanger af11-sanger add column listing crispr IDs in case there are more than 2 d36c4cf
@af11-sanger af11-sanger Merge branch 'devel' of into devel 2643f27
@tg6 tg6 Merge branch 'devel' of into devel de6b4bb
@af11-sanger af11-sanger add hide traces button to crispr QC view 62f2363
Commits on Jul 23, 2015
@af11-sanger af11-sanger add splice acceptor count to frameshift count afd3795
@af11-sanger af11-sanger fixed some bugs causing traceview search string to differ from trace 84b51f3
@af11-sanger af11-sanger Merge branch 'devel' of into devel a18e99f
Commits on Jul 27, 2015
@af11-sanger af11-sanger only consider the best alignment for each read when generating qc run…
… summary results
@af11-sanger af11-sanger stop perlcritic complaining about sub prototyping b9ff8d1
Commits on Jul 28, 2015
@af11-sanger af11-sanger use custom genoverse tracks to ensure they behave the same in all gen…
…overse views
Commits on Jul 29, 2015
@af11-sanger af11-sanger added genoverse crispr group and primer tracks 0d770ea
@PeterFCKeen PeterFCKeen Added primer generation on crispr import from wge 7dfcc59
@PeterFCKeen PeterFCKeen Merge branch 'devel' into peter 68fc1ad
@af11-sanger af11-sanger Merge branch 'genoverse_tidy' into devel d73717c
@af11-sanger af11-sanger plasmid maps added to qc test result view (work in progress...) 4849d87
Commits on Jul 30, 2015
@PeterFCKeen PeterFCKeen Changes to wge import testing script 2261ff9
@af11-sanger af11-sanger added reads to plasmid viewer 9c1d63b
@af11-sanger af11-sanger moved some plasmid display processing logic out of template toolkit. …
…fixed read overlap display issue
@PeterFCKeen PeterFCKeen Changes made to test to include new hyperlink 65f337b
@PeterFCKeen PeterFCKeen v0.329
Improved genoverse views
0.329     2015-07-22 10:45:33 Europe/London

    Sponsor front page sub-report updated:
    - Added splice_acceptor calls to the frameshift counts
    - het clones make a green project checkpoint
    - failed project always turn red most recent checkpoint
@PeterFCKeen PeterFCKeen v0.330 3dd3b15
@af11-sanger af11-sanger added alignment target regions to plasmid view b439f9a
@tg6 tg6 Added Het Summary report 3ef1f3a
@tg6 tg6 Merge branch 'devel' of into devel c0ed4ea
@af11-sanger af11-sanger moved plasmid view related logic into Util module e73867d
Commits on Jul 31, 2015
@tg6 tg6 cleanup of test 1a63b6e
@tg6 tg6 added LIMS2_PRIMER_DIR to 0f885bd
Commits on Aug 03, 2015
@af11-sanger af11-sanger do not show plasmid view for es cell qc. catch plasmid view generatio…
…n errors
@af11-sanger af11-sanger added help link describing example plasmid view 45e0bd9
@af11-sanger af11-sanger Merge branch 'devel' into plasmid_viewer 48deb40
Commits on Aug 04, 2015
@af11-sanger af11-sanger added assembly QC verified column to plate report. it is updated on t…
…he fly using js. cannot get the same to work in extjs version of report
Commits on Aug 05, 2015
@af11-sanger af11-sanger update QC verified value in assembly plate view extjs grid b1e223a
@af11-sanger af11-sanger update extjs record with new qc verified vlue 464abef
@af11-sanger af11-sanger stop uninitialized value warning b390009
@af11-sanger af11-sanger Merge branch 'devel' 62ac10a
@af11-sanger af11-sanger v0.331
   Het summary report added
   Vector QC plasmid maps added to result view
   Assembly plate QC verified status flag added
Commits on Aug 06, 2015
@tg6 tg6 added pcr_done to HetSummary report b636144
@tg6 tg6 fixed broken link. uniformization of buttons 5f83140
@tg6 tg6 cached sponsor sub reports now wide e7c07c3
Commits on Aug 10, 2015
@PeterFCKeen PeterFCKeen Merge branch 'devel' f54f1e8
@PeterFCKeen PeterFCKeen Removed debugging tool from script 7ac8619
@PeterFCKeen PeterFCKeen v0.332 8ca30ab
Commits on Aug 11, 2015
@af11-sanger af11-sanger added some extra methods to check region around primers fc1b04c
@af11-sanger af11-sanger pass file server URL to ListLatestRuns module db85a29
Commits on Aug 12, 2015
@af11-sanger af11-sanger fetch error files via file server api 208e283
@tg6 tg6 updated wide front page cached reports c5c3187
@tg6 tg6 Merge branch 'devel' of into devel 2595658
@tg6 tg6 Merge branch 'devel' 71176c3
@tg6 tg6 v0.332
    Front page report wide view update
    Extra methods to check region around primers
@tg6 tg6 v0.333
    Front page report wide view update
    Extra methods to check region around primers
@af11-sanger af11-sanger use new env variable to specify lustre primer dir if running primer g…
…eneration on farm
Commits on Aug 13, 2015
@af11-sanger af11-sanger use the same BWA ref genomes as HTGT QC Util 417a818
Commits on Aug 19, 2015
@af11-sanger af11-sanger always run primer generation locally instead of using farm c73023b
@tg6 tg6 removed Switch feature usage from 370fe56
Commits on Aug 20, 2015
@tg6 tg6 sponsor sub report: het counts are now empty when no pcr has been che…
…cked in
Commits on Aug 21, 2015
@PeterFCKeen PeterFCKeen Added search crisprs by sequence and validation tags to public reports b5d425d
@PeterFCKeen PeterFCKeen Merge branch 'master' of 479d9fb
@PeterFCKeen PeterFCKeen v0.334
    Search crisprs by sequence feature added
    Crispr primer validation checks added to public reports
@tg6 tg6 CrisprPlateOrderSheet updated to show other wells using the crispr afc07fe
@tg6 tg6 Merge branch 'master' into devel d9413d6
@tg6 tg6 small improvements to Search crisprs by sequence f6f6acd
Commits on Aug 24, 2015
@tg6 tg6 design_target_gene_search default crispr type changed to group 9a5bf07
Commits on Aug 27, 2015
@af11-sanger af11-sanger added interface to create point mutation design from user supplied co…
…ords and sequence
@af11-sanger af11-sanger new design type and oligo type for point mutation designs 7f24abf
Commits on Sep 01, 2015
@af11-sanger af11-sanger trailing space tidy up 44d9bdd
@af11-sanger af11-sanger catch error if traceserver is down and log to console 2507418
Commits on Sep 02, 2015
@af11-sanger af11-sanger show additional environment variables ecde340
@af11-sanger af11-sanger delete fixture data from plate crispr appends e69b724
@af11-sanger af11-sanger workflow change so FP can be frozen back to a single PIQ QC well and …
…fruther FP wells created from this
Commits on Sep 03, 2015
@af11-sanger af11-sanger Merge branch 'devel' into no_lustre dab504d
@af11-sanger af11-sanger perlcritic and test fixes 745e089