All File Changes

v314_preview to v314_preview2 (2015-03-16 to 2015-03-23) v314

• src/hg/cirm/cdw/cdwChangeAccess/cdwChangeAccess.c
  • lines changed 143, context: html, text, full: html, text
    Utility to change access attributes of files matching a query seems to work.
    
• src/hg/cirm/cdw/cdwChangeAccess/makefile
  • lines changed 4, context: html, text, full: html, text
    Utility to change access attributes of files matching a query seems to work.
    
• src/hg/cirm/cdw/cdwCreateGroup/cdwCreateGroup.c
  • lines changed 46, context: html, text, full: html, text
    Making utility to add a group.
    
• src/hg/cirm/cdw/cdwCreateGroup/makefile
  • lines changed 4, context: html, text, full: html, text
    Making utility to add a group.
    
• src/hg/cirm/cdw/cdwFreen/cdwFreen.c
  • lines changed 49, context: html, text, full: html, text
    Adding testing helper.
    
  • lines changed 29, context: html, text, full: html, text
    Making cdwQuickCheckAccess for quicker checking when doing more than one file. Breakeven point at a guess is about 5 files. It gets about 100x faster for thousands of files though.
    
  • lines changed 86, context: html, text, full: html, text
    Exploring a little how to merge different meta.txt files.
    
  • lines changed 81, context: html, text, full: html, text
    Making it just print out list of all fields.
    
  • lines changed 8, context: html, text, full: html, text
    cdwFreen prints out table description.
    
• src/hg/cirm/cdw/cdwFreen/makefile
  • lines changed 4, context: html, text, full: html, text
    Adding testing helper.
    
• src/hg/cirm/cdw/cdwGroupFile/cdwGroupFile.c
  • lines changed 110, context: html, text, full: html, text
    Utility to add group associations to files seems to work.
    
  • lines changed 19, context: html, text, full: html, text
    Simplifying command line so you just need the boolean part of the where clause.
    
  • lines changed 22, context: html, text, full: html, text
    Adding remove option.
    
• src/hg/cirm/cdw/cdwGroupFile/makefile
  • lines changed 4, context: html, text, full: html, text
    Utility to add group associations to files seems to work.
    
• src/hg/cirm/cdw/cdwGroupUser/cdwGroupUser.c
  • lines changed 83, context: html, text, full: html, text
    Utility to add users to a group seems to work.
    
  • lines changed 3, context: html, text, full: html, text
    Saving a couple of lines of code by using a library routine.
    
  • lines changed 35, context: html, text, full: html, text
    Adding remove option.
    
• src/hg/cirm/cdw/cdwGroupUser/makefile
  • lines changed 4, context: html, text, full: html, text
    Utility to add users to a group seems to work.
    
• src/hg/cirm/cdw/cdwMakeEnrichments/cdwMakeEnrichments.c
  • lines changed 7, context: html, text, full: html, text
    Making program not worry about a few new types.
    
• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 1, context: html, text, full: html, text
    Avoiding crash on null assembly for vcf.
    
• src/hg/cirm/cdw/cdwMakeWigSpotQa/cdwMakeWigSpotQa.c
  • lines changed 124, context: html, text, full: html, text
    Removing cwwMakeWigSpotQa, since doesn't compile and can look at code in edwMakeWigSpotQa.
    
• src/hg/cirm/cdw/cdwMakeWigSpotQa/makefile
  • lines changed 4, context: html, text, full: html, text
    Removing cwwMakeWigSpotQa, since doesn't compile and can look at code in edwMakeWigSpotQa.
    
• src/hg/cirm/cdw/cdwQuery/cdwQuery.c
  • lines changed 14, context: html, text, full: html, text
    Making it output a header line when out=tab. Rearranged sort so * is still alphabetical, but when fields are explicitly listed the listed order is kept. Things are only alphabetically ordered within a wildcard expansion of the field list.
    
  • lines changed 2, context: html, text, full: html, text
    Saving a line of code by using a newr library routine.
    
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 28, context: html, text, full: html, text
    Implementing first pass of file access control including login system (hgLogin) and user/group/all access controls, a system for managing groups for access, and overviews of access on the web display home page, and access controlling Genome Browser links elsewhere in the web display.
    
  • lines changed 21, context: html, text, full: html, text
    Having it revalidate when metadata pointed to by metaId changes. Adding command line option to not revalidate. Removing unused 'believe' command line option.
    
• src/hg/cirm/cdw/cdwTextForIndex/cdwTextForIndex.c
  • lines changed 121, context: html, text, full: html, text
    Utility that creates full text index for cdwFileTags seems to work.
    
  • lines changed 6, context: html, text, full: html, text
    Making numerical ID rather than accession be used to in search results.
    
• src/hg/cirm/cdw/cdwTextForIndex/makefile
  • lines changed 4, context: html, text, full: html, text
    Utility that creates full text index for cdwFileTags seems to work.
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwNavBar.html
  • lines changed 4, context: html, text, full: html, text
    Implementing first pass of file access control including login system (hgLogin) and user/group/all access controls, a system for managing groups for access, and overviews of access on the web display home page, and access controlling Genome Browser links elsewhere in the web display.
    
  • lines changed 1, context: html, text, full: html, text
    Added doTest command.
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 2, context: html, text, full: html, text
    Adding chrom back in track table and bumping version.
    
  • lines changed 94, context: html, text, full: html, text
    Implementing first pass of file access control including login system (hgLogin) and user/group/all access controls, a system for managing groups for access, and overviews of access on the web display home page, and access controlling Genome Browser links elsewhere in the web display.
    
  • lines changed 4, context: html, text, full: html, text
    Making cdwQuickCheckAccess for quicker checking when doing more than one file. Breakeven point at a guess is about 5 files. It gets about 100x faster for thousands of files though.
    
  • lines changed 76, context: html, text, full: html, text
    Restricting files and tracks and tags browsing to files you have access to.
    
  • lines changed 66, context: html, text, full: html, text
    Restricting oneTag page to only showing info from accessible files. Changing home page total size reports to use GB, TB, PB rather than full number with many commas. Fixed bug when clicking on links on an item that was abbreviated to fit in a table.
    
  • lines changed 86, context: html, text, full: html, text
    Working on two main features - printing a line of descriptive text about a tag in the doOneTag page, and experimenting with javascript autosuggest for filters.
    
  • lines changed 114, context: html, text, full: html, text
    Putting suggest onto the filters controls where appropriate. Tinkering with test page a little.
    
  • lines changed 91, context: html, text, full: html, text
    Speeding up code that generates suggestions a bunch by making it use cdwFileTags rather than making a tagStorm.
    
  • lines changed 16, context: html, text, full: html, text
    Fixing browse files when there are accessible files, which I just had broken fixing browser files when there are no accessible files.
    
  • lines changed 10, context: html, text, full: html, text
    Trying new watermark code on test page. Seems to work.
    
  • lines changed 30, context: html, text, full: html, text
    Checking out some of the available graphics in the test page and bumping versino number.
    
  • lines changed 135, context: html, text, full: html, text
    Swapping out list of graphic images in test for a pie experiment, and then integrating pie chart into main page.
    
  • lines changed 73, context: html, text, full: html, text
    Implementing trix search. Polishing pie charts on home page.
    
  • lines changed 14, context: html, text, full: html, text
    Making URL an actual link in doLabs page.
    
• src/hg/cirm/cdw/cdwWebBrowse/makefile
  • lines changed 3, context: html, text, full: html, text
    Fixing it so touching .html file remakes .c as well as .h
    
  • lines changed 1, context: html, text, full: html, text
    Working on two main features - printing a line of descriptive text about a tag in the doOneTag page, and experimenting with javascript autosuggest for filters.
    
• src/hg/cirm/cdw/cdwWebBrowse/tagDescriptions.h
  • lines changed 46, context: html, text, full: html, text
    Working on two main features - printing a line of descriptive text about a tag in the doOneTag page, and experimenting with javascript autosuggest for filters.
    
  • lines changed 53, context: html, text, full: html, text
    Second pass at tag descriptions.
    
• src/hg/cirm/cdw/inc/cdw.h
  • lines changed 208, context: html, text, full: html, text
    Implementing first pass of file access control including login system (hgLogin) and user/group/all access controls, a system for managing groups for access, and overviews of access on the web display home page, and access controlling Genome Browser links elsewhere in the web display.
    
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 3, context: html, text, full: html, text
    Making utility to add a group.
    
  • lines changed 22, context: html, text, full: html, text
    Implementing first pass of file access control including login system (hgLogin) and user/group/all access controls, a system for managing groups for access, and overviews of access on the web display home page, and access controlling Genome Browser links elsewhere in the web display.
    
  • lines changed 17, context: html, text, full: html, text
    Making cdwQuickCheckAccess for quicker checking when doing more than one file. Breakeven point at a guess is about 5 files. It gets about 100x faster for thousands of files though.
    
  • lines changed 6, context: html, text, full: html, text
    Adding routines to get list of all good cdwFiles, and also to limit tag storm to what a user can access.
    
  • lines changed 3, context: html, text, full: html, text
    Adding cdwAccessibleFileList function to get list of all accessible files for a users.
    
  • lines changed 3, context: html, text, full: html, text
    Refactoring to expose cdwUserTagStormFromList function, which will help keep us from generating some expensive data structures twice.
    
  • lines changed 5, context: html, text, full: html, text
    Librarifying accessForUser to become cdwAccessTreeForUser thinking it might get reused.
    
• src/hg/cirm/cdw/lib/cdw.as
  • lines changed 26, context: html, text, full: html, text
    Implementing first pass of file access control including login system (hgLogin) and user/group/all access controls, a system for managing groups for access, and overviews of access on the web display home page, and access controlling Genome Browser links elsewhere in the web display.
    
• src/hg/cirm/cdw/lib/cdw.c
  • lines changed 470, context: html, text, full: html, text
    Implementing first pass of file access control including login system (hgLogin) and user/group/all access controls, a system for managing groups for access, and overviews of access on the web display home page, and access controlling Genome Browser links elsewhere in the web display.
    
• src/hg/cirm/cdw/lib/cdw.sql
  • lines changed 31, context: html, text, full: html, text
    Implementing first pass of file access control including login system (hgLogin) and user/group/all access controls, a system for managing groups for access, and overviews of access on the web display home page, and access controlling Genome Browser links elsewhere in the web display.
    
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 8, context: html, text, full: html, text
    Making utility to add a group.
    
  • lines changed 61, context: html, text, full: html, text
    Implementing first pass of file access control including login system (hgLogin) and user/group/all access controls, a system for managing groups for access, and overviews of access on the web display home page, and access controlling Genome Browser links elsewhere in the web display.
    
  • lines changed 85, context: html, text, full: html, text
    Making cdwQuickCheckAccess for quicker checking when doing more than one file. Breakeven point at a guess is about 5 files. It gets about 100x faster for thousands of files though.
    
  • lines changed 17, context: html, text, full: html, text
    Adding routines to get list of all good cdwFiles, and also to limit tag storm to what a user can access.
    
  • lines changed 36, context: html, text, full: html, text
    Adding cdwAccessibleFileList function to get list of all accessible files for a users.
    
  • lines changed 19, context: html, text, full: html, text
    Librarifying accessForUser to become cdwAccessTreeForUser thinking it might get reused.
    
• src/hg/cirm/cdw/lib/cdwTagStorm.c
  • lines changed 45, context: html, text, full: html, text
    Adding info from cdwVcfFile to storm. Calculating amount of vcf that is explained by common snps by looking up common_snp in cdwEnrich.
    
  • lines changed 46, context: html, text, full: html, text
    Adding routines to get list of all good cdwFiles, and also to limit tag storm to what a user can access.
    
  • lines changed 21, context: html, text, full: html, text
    Refactoring to expose cdwUserTagStormFromList function, which will help keep us from generating some expensive data structures twice.
    
  • lines changed 19, context: html, text, full: html, text
    Librarifying accessForUser to become cdwAccessTreeForUser thinking it might get reused.
    
  • lines changed 4, context: html, text, full: html, text
    Fixing a bug where was crashing if you weren't logged in.
    
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 1, context: html, text, full: html, text
    Correcting age_unit to be singular the way t_unit is.
    
  • lines changed 8, context: html, text, full: html, text
    Making use of periods more consistent in descriptions.
    
• src/hg/cirm/cdw/makefile
  • lines changed 5, context: html, text, full: html, text
    Removing cwwMakeWigSpotQa, since doesn't compile and can look at code in edwMakeWigSpotQa.
    
• src/hg/cirm/cdw/utils/cdwVcfStats/cdwVcfStats.c
  • lines changed 1, context: html, text, full: html, text
    Doing little bit of resource freeing, but not to matter in the absense of a vcfRecordFree. This utility currently leaks memory. On the 1000 genomes data was up to using 400 Gig on chr1 before I killed it.
    
  • lines changed 19, context: html, text, full: html, text
    Commenting out some statistics gathering that I feared was making things too slow. Making it free up memory from time to time.
    
• src/hg/hgAi/hgAi.c
  • lines changed 330, context: html, text, full: html, text
    Renaming hgAi to hgIntegrator by popular demand.
    
• src/hg/hgAi/makefile
  • lines changed 17, context: html, text, full: html, text
    Renaming hgAi to hgIntegrator by popular demand.
    
• src/hg/hgBeacon/makefile
  • lines changed 3, context: html, text, full: html, text
    Fixing a makefile's assumption that /gbdb/hg19/beacon exists.
    
  • lines changed 6, context: html, text, full: html, text
    fixing merge conflict
    
• src/hg/hgChooseDb/hgChooseDb.c
  • lines changed 1, context: html, text, full: html, text
    Renaming hgAi to hgIntegrator by popular demand.
    
• src/hg/hgCustom/hgCustom.c
  • lines changed 27, context: html, text, full: html, text
    bigGenePred doc
    
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 330, context: html, text, full: html, text
    Renaming hgAi to hgIntegrator by popular demand.
    
• src/hg/hgIntegrator/makefile
  • lines changed 15, context: html, text, full: html, text
    Renaming hgAi to hgIntegrator by popular demand.
    
• src/hg/hgLogin/hgLogin.c
  • lines changed 5, context: html, text, full: html, text
    Moving cartSaveSession() to inside of a form so that it actually does save the session ID.
    
  • lines changed 23, context: html, text, full: html, text
    Making it deal with situations like under a VPN where the web address is not qualified with . anything, and effectively there is thus no domain to use for the cookies.
    
• src/hg/hgTables/greatData/supportedAssemblies.txt
  • lines changed 2, context: html, text, full: html, text
    Adding GREAT support for mm10, removing support for hg18, refs #14881
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1838, context: html, text, full: html, text
    bigGenePred doc
    
  • lines changed 1835, context: html, text, full: html, text
    rewind check-in of ancient version of simpleTracks.c that git decided I
    wanted to check in.
    
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 39, context: html, text, full: html, text
    bigGenePred doc
    
  • lines changed 1, context: html, text, full: html, text
    a couple of typos in bigGenePred doc
    
• src/hg/htdocs/Neandertal/index.html
  • lines changed 1, context: html, text, full: html, text
    switching pointers from CBSE to GI website. refs #14220
    
  • lines changed 2, context: html, text, full: html, text
    changing menu from ENCODE to Ebola to match the same menu on the home page
    
• src/hg/htdocs/goldenPath/help/bigGenePred.html
  • lines changed 219, context: html, text, full: html, text
    bigGenePred doc
    
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 1, context: html, text, full: html, text
    bigGenePred doc
    
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 17, context: html, text, full: html, text
    update to gbib docs, refs #15022
    
  • lines changed 2, context: html, text, full: html, text
    gbib doc update, refs #15002
    
  • lines changed 10, context: html, text, full: html, text
    a little clean-up but mostly breaking the lines to less than 100 chars
    
• src/hg/htdocs/goldenPath/help/hgAiHelp.html
  • lines changed 56, context: html, text, full: html, text
    Renaming hgAi to hgIntegrator by popular demand.
    
• src/hg/htdocs/goldenPath/help/hgIntegratorHelp.html
  • lines changed 56, context: html, text, full: html, text
    Renaming hgAi to hgIntegrator by popular demand.
    
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 15, context: html, text, full: html, text
    bigGenePred doc
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 24, context: html, text, full: html, text
    adding announcement for new RM Viz track, refs #9741
    
  • lines changed 2, context: html, text, full: html, text
    Changing link to track description page in announcement
    
  • lines changed 1, context: html, text, full: html, text
    Fixing spelling error in RM Viz announcement
    
• src/hg/htdocs/images/Nanorana_parkeri.jpg
  • lines changed 0, context: html, text, full: html, text
    photo courtesy Copyright (C) 2013 Kai Wang http://wangwenzhiwen.blog.163.com/ refs #14560
    
• src/hg/htdocs/images/stem-cell-talk-57210.jpg
  • lines changed 0, context: html, text, full: html, text
    Adding a stem cell photo.
    
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    starting to fix the many many instances where we should be pointing to the new Genomics Institute site instead of CBSE. refs #14220
    
• src/hg/htdocs/index.html
  • lines changed 1, context: html, text, full: html, text
    starting to fix the many many instances where we should be pointing to the new Genomics Institute site instead of CBSE. refs #14220
    
• src/hg/htdocs/indexIntro.html
  • lines changed 3, context: html, text, full: html, text
    switching pointers from CBSE to GI website
    
• src/hg/htdocs/indexNews.html
  • lines changed 59, context: html, text, full: html, text
    adding announcement for new RM Viz track, refs #9741
    
  • lines changed 2, context: html, text, full: html, text
    Fixing up awkward archive announcement for youtube vid
    
  • lines changed 2, context: html, text, full: html, text
    Changing link to track description page in announcement
    
  • lines changed 1, context: html, text, full: html, text
    Fixing spelling error in RM Viz announcement
    
• src/hg/htdocs/staff.html
  • lines changed 1, context: html, text, full: html, text
    switching pointers from CBSE to GI website
    
• src/hg/inc/hCommon.h
  • lines changed 1, context: html, text, full: html, text
    Renaming hgAi to hgIntegrator by popular demand.
    
• src/hg/inc/tablesTables.h
  • lines changed 1, context: html, text, full: html, text
    Adding 'shortVal' parameter to webTableOutputWrapperType. This is so can use the full value for constructing urls and the like, but display the short value in the table so as to keep it from getting too wide.
    
  • lines changed 2, context: html, text, full: html, text
    Adding suggestHash to tables so they can do suggestions.
    
• src/hg/inc/wikiLink.h
  • lines changed 6, context: html, text, full: html, text
    A little refactoring so can reuse login system for CIRM.
    
• src/hg/js/cdwPersona.js
  • lines changed 45, context: html, text, full: html, text
    No need for persona in cdw it looks like.
    
• src/hg/js/cdwSuggest.js
  • lines changed 85, context: html, text, full: html, text
    Exploring some suggest stuff in CIRM data warehouse.
    
  • lines changed 1, context: html, text, full: html, text
    Some tinkering, but generally looks like won't be using this module for long. Most of the logic has moved.
    
  • lines changed 86, context: html, text, full: html, text
    No longer useing cdwSuggest.js
    
• src/hg/js/d3pie.min.js
  • lines changed 9, context: html, text, full: html, text
    Adding a pie chart maker that is pretty nice and depends on D3.
    
• src/hg/js/jquery.watermark.js
  • lines changed 625, context: html, text, full: html, text
    Adding a watermark (grayed out text to serve as mini-instructions in a text input control) from a jquery library that's better about not submitting the watermark than the older jquery.watermarkinput.gs.
    
  • lines changed 0, context: html, text, full: html, text
    Removed DOS CRLF
    
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    Exploring some suggest stuff in CIRM data warehouse.
    
  • lines changed 1, context: html, text, full: html, text
    No longer useing cdwSuggest.js
    
  • lines changed 1, context: html, text, full: html, text
    Adding a watermark (grayed out text to serve as mini-instructions in a text input control) from a jquery library that's better about not submitting the watermark than the older jquery.watermarkinput.gs.
    
• src/hg/js/model/hgAi/hgAiModel.js
  • lines changed 667, context: html, text, full: html, text
    Renaming hgAi to hgIntegrator by popular demand.
    
• src/hg/js/model/hgAi/makefile
  • lines changed 7, context: html, text, full: html, text
    Renaming hgAi to hgIntegrator by popular demand.
    
• src/hg/js/model/hgChooseDb/hgChooseDbModel.js
  • lines changed 1, context: html, text, full: html, text
    Renaming hgAi to hgIntegrator by popular demand.
    
• src/hg/js/model/hgIntegrator/hgIntegratorModel.js
  • lines changed 667, context: html, text, full: html, text
    Renaming hgAi to hgIntegrator by popular demand.
    
• src/hg/js/model/hgIntegrator/makefile
  • lines changed 7, context: html, text, full: html, text
    Renaming hgAi to hgIntegrator by popular demand.
    
• src/hg/js/model/makefile
  • lines changed 1, context: html, text, full: html, text
    Renaming hgAi to hgIntegrator by popular demand.
    
• src/hg/js/react/hgAi/hgAi.jsx
  • lines changed 493, context: html, text, full: html, text
    Renaming hgAi to hgIntegrator by popular demand.
    
• src/hg/js/react/hgAi/makefile
  • lines changed 12, context: html, text, full: html, text
    Renaming hgAi to hgIntegrator by popular demand.
    
• src/hg/js/react/hgChooseDb/hgChooseDb.jsx
  • lines changed 2, context: html, text, full: html, text
    Renaming hgAi to hgIntegrator by popular demand.
    
• src/hg/js/react/hgIntegrator/hgIntegrator.jsx
  • lines changed 493, context: html, text, full: html, text
    Renaming hgAi to hgIntegrator by popular demand.
    
• src/hg/js/react/hgIntegrator/makefile
  • lines changed 12, context: html, text, full: html, text
    Renaming hgAi to hgIntegrator by popular demand.
    
• src/hg/js/react/makefile
  • lines changed 1, context: html, text, full: html, text
    Renaming hgAi to hgIntegrator by popular demand.
    
• src/hg/lib/bigPsl.as
  • lines changed 34, context: html, text, full: html, text
    first cut at bigPsl format
    
  • lines changed 11, context: html, text, full: html, text
    changing the format of bigPsl around a little
    
• src/hg/lib/cart.c
  • lines changed 7, context: html, text, full: html, text
    Making it work behind a firewall/VPN where there is effectively no domain.
    
• src/hg/lib/hCommon.c
  • lines changed 3, context: html, text, full: html, text
    Renaming hgAi to hgIntegrator by popular demand.
    
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    Fixing something that slipped by me in code review and affects only my
    new code (cartJson.c is the only file that calls the affected function, hGetCladeOptions).
    
• src/hg/lib/hubConnect.c
  • lines changed 2, context: html, text, full: html, text
    increase the size of some buffers
    
• src/hg/lib/omiciaUi.c
  • lines changed 55, context: html, text, full: html, text
    Adding up or down arrow after a column we sort on.
    
  • lines changed 55, context: html, text, full: html, text
    Oops, did not mean to add these!
    
• src/hg/lib/oregannoOther.c
  • lines changed 591, context: html, text, full: html, text
    Adding up or down arrow after a column we sort on.
    
  • lines changed 591, context: html, text, full: html, text
    Oops, did not mean to add these!
    
• src/hg/lib/tablesTables.c
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    Adding 'shortVal' parameter to webTableOutputWrapperType. This is so can use the full value for constructing urls and the like, but display the short value in the table so as to keep it from getting too wide.
    
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    Starting to have suggest javascript going on in filter row
    
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    Adding suggestHash to tables so they can do suggestions.
    
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    Putting in but then ifdefing out some watermark code that looked nice, but left the word 'filter' printed all over the cart. Will try and fix soon. Wordsmithing one line of instructions a little.
    
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    Trying another shot at watermarks on the filter row. Seems to work with new library.
    
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    Adding up or down arrow after a column we sort on.
    
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    Making it print numerical fields right justified. Tweaking instructiona line a little.
    
• src/hg/lib/wikiLink.c
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    A little refactoring so can reuse login system for CIRM.
    
• src/hg/makeDb/doc/danRer10/initialBuild.txt
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    add blat server refs #14017
    
• src/hg/makeDb/doc/felCat8/initialBuild.txt
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    add blat server refs #14412
    
• src/hg/makeDb/doc/macFas5/initialBuild.txt
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    add blat server refs #11174
    
• src/hg/makeDb/doc/nanPar1/initialBuild.txt
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    starting Tibetian frog browser build refs #14560
    
• src/hg/makeDb/doc/nasLar1/initialBuild.txt
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    add blat server refs #14437
    
• src/hg/makeDb/doc/panPan1.txt
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    add blat server refs #11348
    
• src/hg/makeDb/doc/proteins/150225.txt
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    finish up proteome database build
    
• src/hg/makeDb/doc/uniProt/sp150225.txt
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    struggling to get the UniProt database to build
    
• src/hg/makeDb/doc/xenTro3.txt
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    xenTro7 in the pushQ refs #9868
    
• src/hg/makeDb/doc/xenTro7.txt
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    xenTro7 in the pushQ refs #9868
    
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    xenTro7 in the pushQ refs #9868
    
• src/hg/makeDb/schema/dbSnoop/dbSnoop.c
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    Adding skipTable option.
    
• src/hg/makeDb/trackDb/armadillo/dasNov3/description.html
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    changing links on armadillo (dasNov3) track description pages
    
• src/hg/makeDb/trackDb/armadillo/dasNov3/gap.html
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    changing links on armadillo (dasNov3) track description pages
    
• src/hg/makeDb/trackDb/armadillo/dasNov3/gold.html
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    changing links on armadillo (dasNov3) track description pages
    
• src/hg/makeDb/trackDb/cow/bosTau4/multiz5way.html
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    Changing links on track description pages for bosTau4, fr3, myoLuc2
    
• src/hg/makeDb/trackDb/drosophila/dm1/flyreg.html
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    changing links on drosophila (dm1, droSim1, droVir2) track description pages
    
• src/hg/makeDb/trackDb/drosophila/droSim1/description.html
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    changing links on drosophila (dm1, droSim1, droVir2) track description pages
    
• src/hg/makeDb/trackDb/drosophila/droSim1/gold.html
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    changing links on drosophila (dm1, droSim1, droVir2) track description pages
    
• src/hg/makeDb/trackDb/drosophila/droVir2/description.html
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    changing links on drosophila (dm1, droSim1, droVir2) track description pages
    
• src/hg/makeDb/trackDb/drosophila/droVir2/gap.html
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    changing links on drosophila (dm1, droSim1, droVir2) track description pages
    
• src/hg/makeDb/trackDb/frog/nanPar1/description.html
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    adding nanPar1 Tibetian frog to the build refs #14560
    
• src/hg/makeDb/trackDb/frog/nanPar1/gap.html
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    adding nanPar1 Tibetian frog to the build refs #14560
    
• src/hg/makeDb/trackDb/frog/nanPar1/gold.html
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    adding nanPar1 Tibetian frog to the build refs #14560
    
• src/hg/makeDb/trackDb/frog/nanPar1/trackDb.ra
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    adding nanPar1 Tibetian frog to the build refs #14560
    
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    add assembly/gold track search rule refs #14560
    
• src/hg/makeDb/trackDb/fugu/fr3/cons8way.html
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    Changing links on track description pages for bosTau4, fr3, myoLuc2
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.cacTest100way.ra
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    default vis hide refs #11636
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    cacTest include for alpha only refs #11636
    
• src/hg/makeDb/trackDb/joinedRmsk.ra
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    Adding canPack for RM Viz track on beta, track is broken without it. refs #9741
    
• src/hg/makeDb/trackDb/makefile
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    adding nanPar1 Tibetian frog to the build refs #14560
    
• src/hg/makeDb/trackDb/microbat/myoLuc2/description.html
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    Changing links on track description pages for bosTau4, fr3, myoLuc2
    
• src/hg/makeDb/trackDb/mouse/mm9/NIAGene.html
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    changing links on mouse (mm9) track description pages
    
• src/hg/makeDb/trackDb/mouse/mm9/allMm9RS_BW.html
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    changing links on mouse (mm9) track description pages
    
• src/hg/makeDb/trackDb/mouse/mm9/laminB1Mm9.html
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    changing links on mouse (mm9) track description pages
    
• src/hg/makeDb/trackDb/mouse/mm9/rest.html
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    changing links on mouse (mm9) track description pages
    
• src/hg/makeDb/trackDb/wgEncodeNhgriBip.html
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    changing links on mouse (mm9) track description pages
    
• src/hg/makeDb/trackDb/worm/caeRem2/description.html
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    Changing links on worm (caeRem2, ce2) track description pages
    
• src/hg/makeDb/trackDb/worm/ce2/wabaCbr.html
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    Changing links on worm (caeRem2, ce2) track description pages
    
• src/hg/makeDb/trackDb/xenTro/xenTro2/description.html
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    changing links on X tropicalis (xenTro2) track description pages
    
• src/hg/makeDb/trackDb/xenTro/xenTro2/multiz7way.html
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    changing links on X tropicalis (xenTro2) track description pages
    
• src/hg/makeDb/trackDb/xenTro/xenTro7/trackDb.ra
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    adding search rule for gold table refs #9868
    
• src/hg/makeDb/trackDb/zebrafish/danRer3/bacEndPairs.html
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    changing links on zebrafish (danRer3) track description pages
    
• src/hg/makeDb/trackDb/zebrafish/danRer3/bacEndSingles.html
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    changing links on zebrafish (danRer3) track description pages
    
• src/hg/makeDb/trackDb/zebrafish/danRer3/multiz5way.html
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    changing links on zebrafish (danRer3) track description pages
    
• src/hg/makefile
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    add some Rna utils to the userApps refs #14513
    
• src/hg/oneShot/freen/freen.c
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    Freen does reality speed check on loading all exons for a chrom into a rangeTree.
    
• src/hg/protein/spToDb/spDb.sql
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    struggling to get the UniProt database to build
    
• src/hg/protein/spToDb/spToDb.c
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    struggling to get the UniProt database to build
    
• src/hg/protein/stripEvidence/makefile
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    struggling to get the UniProt database to build
    
• src/hg/protein/stripEvidence/stripEvidence.c
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    struggling to get the UniProt database to build
    
• src/hg/utils/automation/EnsGeneAutomate.pm
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    adding v79 definitions refs #15005
    
• src/hg/utils/automation/lastz_D/README.txt
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    scripts used for lastz_D tuning procedure refs #14513
    
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    scripts used for lastz_D tuning procedure refs #14513
    
• src/hg/utils/automation/lastz_D/adjustSizes.pl
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    scripts used for lastz_D tuning procedure refs #14513
    
• src/hg/utils/automation/lastz_D/createScoresFileControl.txt
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    scripts used for lastz_D tuning procedure refs #14513
    
• src/hg/utils/automation/lastz_D/expandScoresFile.py
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    scripts used for lastz_D tuning procedure refs #14513
    
• src/hg/utils/automation/lastz_D/mafScoreSizeScan.pl
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    scripts used for lastz_D tuning procedure refs #14513
    
• src/hg/utils/automation/lastz_D/scoreScan.sh
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    scripts used for lastz_D tuning procedure refs #14513
    
• src/hg/utils/automation/lastz_D/selectedFasta.sh
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    scripts used for lastz_D tuning procedure refs #14513
    
• src/hg/utils/automation/lastz_D/topAll.sh
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    scripts used for lastz_D tuning procedure refs #14513
    
• src/hg/utils/gff3ToPsl/gff3ToPsl.c
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    don't assume query and target are the same set of sequences
    
• src/hg/utils/gff3ToPsl/tests/expected/patch1test.psl
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    don't assume query and target are the same set of sequences
    
• src/hg/utils/gff3ToPsl/tests/expected/patch1test.psl.gz
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    don't assume query and target are the same set of sequences
    
• src/hg/utils/gff3ToPsl/tests/input/chrom.sizes
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    don't assume query and target are the same set of sequences
    
• src/hg/utils/gff3ToPsl/tests/input/chrom.sizes.gz
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    don't assume query and target are the same set of sequences
    
• src/hg/utils/gff3ToPsl/tests/input/haploMaps.gff
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    don't assume query and target are the same set of sequences
    
• src/hg/utils/gff3ToPsl/tests/input/haploMaps.gff.gz
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    don't assume query and target are the same set of sequences
    
• src/hg/utils/gff3ToPsl/tests/makefile
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    don't assume query and target are the same set of sequences
    
• src/inc/obscure.h
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    Adding printWithGreekByte, just a wrapper around sprintWithGreekByte.
    
• src/lib/obscure.c
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    Adding printWithGreekByte, just a wrapper around sprintWithGreekByte.
    
• src/tagStorm/tagStormHoist/expected.out
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    Adding a test case.
    
• src/tagStorm/tagStormHoist/test.in
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    Adding a test case.
    
• src/utils/qa/weeklybld/buildEnv.csh
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    v314 preview2 refs #14998
    

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