All File Changes

v315_preview to v315_preview2 (2015-04-08 to 2015-04-13) v315

• src/hg/hgGateway/hgGateway.c
  • lines changed 62, context: html, text, full: html, text
    change mirror redirect to be opt-in.
    
• src/hg/hgGenome/import.c
  • lines changed 9, context: html, text, full: html, text
    Libifying trackDbCmpShortLabel so I can use it elsewhere.
    
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 3, context: html, text, full: html, text
    change mirror redirect to be opt-in.
    
• src/hg/hgSession/hgSession.c
  • lines changed 105, context: html, text, full: html, text
    change mirror redirect to be opt-in.
    
• src/hg/hgTables/bigBed.c
  • lines changed 1, context: html, text, full: html, text
    Better to use hTableExists() as Max pointed out. refs #15126
    
• src/hg/hgTables/correlate.c
  • lines changed 1, context: html, text, full: html, text
    Libifying trackDbCmpShortLabel so I can use it elsewhere.
    
• src/hg/hgTables/hgTables.h
  • lines changed 3, context: html, text, full: html, text
    Libifying trackDbCmpShortLabel so I can use it elsewhere.
    
• src/hg/hgTables/mainPage.c
  • lines changed 9, context: html, text, full: html, text
    Libifying trackDbCmpShortLabel so I can use it elsewhere.
    
• src/hg/hgTracks/adjacencyTrack.c
  • lines changed 493, context: html, text, full: html, text
    another file for little feet mode
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 33, context: html, text, full: html, text
    first go a external tools integration
    
  • lines changed 46, context: html, text, full: html, text
    2nd version of external tools menu support
    
  • lines changed 9, context: html, text, full: html, text
    first cut at little feet mode
    
• src/hg/hgTracks/mainMain.c
  • lines changed 8, context: html, text, full: html, text
    first go a external tools integration
    
  • lines changed 21, context: html, text, full: html, text
    2nd version of external tools menu support
    
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    first cut at little feet mode
    
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 8, context: html, text, full: html, text
    Libifying trackDbCmpShortLabel so I can use it elsewhere.
    
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 4, context: html, text, full: html, text
    made a few corrections per code review #15121
    
  • lines changed 2, context: html, text, full: html, text
    bigGenePred was not in alphabetical order, fixed
    
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 140, context: html, text, full: html, text
    Added info about GRC mouse and zfish sections.
    
  • lines changed 1615, context: html, text, full: html, text
    Part one of updating the credits page (done through Zebrafish). Added reference papers for genomes that have been published, reorganized lists for GB browser credits for each assembly. For paired reviews, this will be too many little changes to go over line by line -- probably best to just eyeball the file on hgwdev-donnak and look for any obvious format errors or typos in the conditions for use sections.
    
• src/hg/htdocs/goldenPath/help/bigGenePred.html
  • lines changed 7, context: html, text, full: html, text
    made a few corrections per code review #15121
    
  • lines changed 1, context: html, text, full: html, text
    corrected link to example file
    
  • lines changed 15, context: html, text, full: html, text
    Small changes to the new bigGenePred html page that could be helpful about chrom.sizes and highlighting bed12+8 input
    
  • lines changed 68, context: html, text, full: html, text
    Adding changes to bigGenePred help page, refs #14376
    
  • lines changed 1, context: html, text, full: html, text
    Small typo fix to bigGenePred html
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 21, context: html, text, full: html, text
    added announcement for bigGenPred
    
  • lines changed 1, context: html, text, full: html, text
    fixed font size and color in news title
    
• src/hg/htdocs/index.html
  • lines changed 6, context: html, text, full: html, text
    Replacing homepage menu with javascript menu from CGIs, refs #14902
    
• src/hg/htdocs/indexNews.html
  • lines changed 45, context: html, text, full: html, text
    added announcement for bigGenPred
    
  • lines changed 4, context: html, text, full: html, text
    fixed spacing in archives section
    
  • lines changed 1, context: html, text, full: html, text
    corrected link to help page
    
• src/hg/htdocs/training/index.html
  • lines changed 54, context: html, text, full: html, text
    made workshop schedule easier to read as a table. added jax labs workshop
    
  • lines changed 1, context: html, text, full: html, text
    made workshop schedule easier to read as a table. added jax labs workshop
    
  • lines changed 5, context: html, text, full: html, text
    Adding ENCODE users meeting. refs #15011
    
  • lines changed 13, context: html, text, full: html, text
    adding UMaine Orono workshop. refs #15011
    
  • lines changed 8, context: html, text, full: html, text
    Alphabetizing some links. refs #15118
    
  • lines changed 5, context: html, text, full: html, text
    added bio_IT World appearance
    
  • lines changed 13, context: html, text, full: html, text
    fixed eshg link to be more specific, add VALIGN tags to TD on dates
    
  • lines changed 6, context: html, text, full: html, text
    Adding an entry for H. Lee Moffitt Cancer Center. refs #15011
    
• src/hg/inc/adjacency.h
  • lines changed 72, context: html, text, full: html, text
    a few more files used for little feet mode
    
• src/hg/inc/cart.h
  • lines changed 4, context: html, text, full: html, text
    change mirror redirect to be opt-in.
    
• src/hg/inc/cartDb.h
  • lines changed 11, context: html, text, full: html, text
    allow for different names for the sessionDb and userDb tables
    
• src/hg/inc/trackDb.h
  • lines changed 3, context: html, text, full: html, text
    Libifying trackDbCmpShortLabel so I can use it elsewhere.
    
• src/hg/inc/web.h
  • lines changed 2, context: html, text, full: html, text
    change mirror redirect to be opt-in.
    
• src/hg/js/model/hgIntegrator/hgIntegratorModel.js
  • lines changed 10, context: html, text, full: html, text
    Handle empty groupedTrackDb more gracefully.
    
• src/hg/js/model/lib/ImModel.js
  • lines changed 2, context: html, text, full: html, text
    Oops, the actual error message from the CGI was not displayed as intended -- fixed. refs #14579 note 31
    
  • lines changed 23, context: html, text, full: html, text
    ImModel: support custom server error handler in cartDo.
    PositionSearch: if server's error message is only the benign "Sorry,
    couldn't find <blah> in genome", just display it to the user instead
    of treating it as a real error from the server.
    refs #14579
    
• src/hg/js/model/lib/PositionSearchMixin.js
  • lines changed 11, context: html, text, full: html, text
    ImModel: support custom server error handler in cartDo.
    PositionSearch: if server's error message is only the benign "Sorry,
    couldn't find <blah> in genome", just display it to the user instead
    of treating it as a real error from the server.
    refs #14579
    
• src/hg/lib/adjacency.as
  • lines changed 13, context: html, text, full: html, text
    a few more files used for little feet mode
    
• src/hg/lib/adjacency.c
  • lines changed 168, context: html, text, full: html, text
    a few more files used for little feet mode
    
• src/hg/lib/bigPsl.as
  • lines changed 3, context: html, text, full: html, text
    add a few more stats to bigPsl record (per Jim)
    
• src/hg/lib/cart.c
  • lines changed 17, context: html, text, full: html, text
    allow for different names for the sessionDb and userDb tables
    
  • lines changed 100, context: html, text, full: html, text
    change mirror redirect to be opt-in.
    
• src/hg/lib/cartDb.c
  • lines changed 28, context: html, text, full: html, text
    allow for different names for the sessionDb and userDb tables
    
• src/hg/lib/cartJson.c
  • lines changed 53, context: html, text, full: html, text
    Matt found that an assembly hub with no track groups (e.g. ThorntonHub)
    caused errors in hgIntegrator. Detect that case and make an "All Tracks"
    group if there are no other groups. refs #14579 note 32
    
• src/hg/lib/customAdjacency.c
  • lines changed 263, context: html, text, full: html, text
    first cut at little feet mode
    
• src/hg/lib/customFactory.c
  • lines changed 4, context: html, text, full: html, text
    first cut at little feet mode
    
• src/hg/lib/hAnno.c
  • lines changed 3, context: html, text, full: html, text
    Better to use hTableExists() as Max pointed out. refs #15126
    
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    changes after code review, refs #15127
    
• src/hg/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    first cut at little feet mode
    
• src/hg/lib/sessionDb.as
  • lines changed 11, context: html, text, full: html, text
    allow for different names for the sessionDb and userDb tables
    
• src/hg/lib/sessionDb.sql
  • lines changed 17, context: html, text, full: html, text
    allow for different names for the sessionDb and userDb tables
    
• src/hg/lib/trackDbCustom.c
  • lines changed 8, context: html, text, full: html, text
    Libifying trackDbCmpShortLabel so I can use it elsewhere.
    
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    Include defaultPos in dbDb from trackHub::makeDbDbFromAssemblyGenome (so cartJson can find it in dbDbs from trackHubGetDbDbs). refs #14579 note 30
    
• src/hg/lib/userDb.as
  • lines changed 11, context: html, text, full: html, text
    allow for different names for the sessionDb and userDb tables
    
• src/hg/lib/userDb.sql
  • lines changed 17, context: html, text, full: html, text
    allow for different names for the sessionDb and userDb tables
    
• src/hg/lib/web.c
  • lines changed 95, context: html, text, full: html, text
    change mirror redirect to be opt-in.
    
• src/hg/makeDb/doc/eboVir2/genePred.txt
  • lines changed 12, context: html, text, full: html, text
    some doc for eboVir2 that I didn't check in long ago
    
• src/hg/makeDb/doc/hg38/multiz20way.txt
  • lines changed 155, context: html, text, full: html, text
    done with 20-way but problems discovered with chain net rheMac3 canFam3 and others refs #14970
    
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes15.csh
  • lines changed 1521, context: html, text, full: html, text
    started ucsc genes for mm10
    
  • lines changed 147, context: html, text, full: html, text
    first cut at a new gene set for mm10
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    add braNey38 to all.joiner
    
• src/hg/makeDb/trackDb/human/hg38/cons20way.html
  • lines changed 464, context: html, text, full: html, text
    adding 20-way definitions refs #14970
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.20way.ra
  • lines changed 103, context: html, text, full: html, text
    adding 20-way definitions refs #14970
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding 20-way definitions refs #14970
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.html
  • lines changed 64, context: html, text, full: html, text
    A html file for lifting that was missed in the last commit
    
  • lines changed 14, context: html, text, full: html, text
    Whitespace changes to hg38 ENCODE track descrption pages.
    
  • lines changed 36, context: html, text, full: html, text
    Edits to hg38 ENCODE Regulation track description pages.
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnase.html
  • lines changed 2, context: html, text, full: html, text
    Whitespace changes to hg38 ENCODE track descrption pages.
    
  • lines changed 18, context: html, text, full: html, text
    Edits to hg38 ENCODE Regulation track description pages.
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnaseClustered.html
  • lines changed 2, context: html, text, full: html, text
    Whitespace changes to hg38 ENCODE track descrption pages.
    
  • lines changed 22, context: html, text, full: html, text
    Edits to hg38 ENCODE Regulation track description pages.
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnaseSignal.html
  • lines changed 6, context: html, text, full: html, text
    Edits to hg38 ENCODE Regulation track description pages.
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegMarkH3k27ac.html
  • lines changed 39, context: html, text, full: html, text
    Html files for lifted tracks
    
  • lines changed 5, context: html, text, full: html, text
    Whitespace changes to hg38 ENCODE track descrption pages.
    
  • lines changed 25, context: html, text, full: html, text
    Edits to hg38 ENCODE Regulation track description pages.
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegMarkH3k4me1.html
  • lines changed 38, context: html, text, full: html, text
    Html files for lifted tracks
    
  • lines changed 8, context: html, text, full: html, text
    Whitespace changes to hg38 ENCODE track descrption pages.
    
  • lines changed 25, context: html, text, full: html, text
    Edits to hg38 ENCODE Regulation track description pages.
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegMarkH3k4me3.html
  • lines changed 38, context: html, text, full: html, text
    Html files for lifted tracks
    
  • lines changed 5, context: html, text, full: html, text
    Whitespace changes to hg38 ENCODE track descrption pages.
    
  • lines changed 26, context: html, text, full: html, text
    Edits to hg38 ENCODE Regulation track description pages.
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegTxn.html
  • lines changed 41, context: html, text, full: html, text
    Html files for lifted tracks
    
  • lines changed 4, context: html, text, full: html, text
    Whitespace changes to hg38 ENCODE track descrption pages.
    
  • lines changed 23, context: html, text, full: html, text
    Edits to hg38 ENCODE Regulation track description pages.
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 17, context: html, text, full: html, text
    fixing release date for DGV track
    
  • lines changed 18, context: html, text, full: html, text
    correcting date for DGV track
    
  • lines changed 2, context: html, text, full: html, text
    fixed release date, hopefully one last time
    
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 2, context: html, text, full: html, text
    removing unneeded copies and fixing the output path of clinvar otto
    update. refs #14045
    
• src/hg/utils/otto/clinvar/doUpdate.sh
  • lines changed 4, context: html, text, full: html, text
    removing unneeded copies and fixing the output path of clinvar otto
    update. refs #14045
    
• src/inc/udc.h
  • lines changed 3, context: html, text, full: html, text
    changes after code review, refs #15127
    
• src/lib/udc.c
  • lines changed 23, context: html, text, full: html, text
    changes after code review, refs #15127
    
• src/oneShot/jsonToTagStorm/jsonToTagStorm.c
  • lines changed 126, context: html, text, full: html, text
    A program that converts .json to .tagStorm, the .json must be in a very specific form
    
  • lines changed 115, context: html, text, full: html, text
    Some very ugly code to convert json to tagStorm format. It is getting awfully large and there is relatively no end in sight..
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v315 preview2 refs #15117
    

• lines changed: 6960
• files changed: 105