All File Changes

v328_base to v329_preview (2016-02-08 to 2016-02-15) v329

• src/hg/cirm/cdw/wrangle/kallistoToMatrix/kallistoToMatrix
  • lines changed 47, context: html, text, full: html, text
    warning about non-chrom transcripts in kallistoToMatrix, also not
    rewriting to symbols anymore, as two gencode genes can share the symbol
    apparently.
    
• src/hg/hgGene/hgGene.c
  • lines changed 1, context: html, text, full: html, text
    renaming malacards.c to malaCards.c by email from Jim. Also changing the
    comments but not the table name, as it has already been pushed to the RR. no redmine.
    
  • lines changed 2, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
• src/hg/hgGene/hgGene.h
  • lines changed 2, context: html, text, full: html, text
    renaming malacards.c to malaCards.c by email from Jim. Also changing the
    comments but not the table name, as it has already been pushed to the RR. no redmine.
    
• src/hg/hgGene/hgGeneData/Human/links.ra
  • lines changed 1, context: html, text, full: html, text
    Updating link to Lynx for hgGene, refs #16649
    
• src/hg/hgGene/makefile
  • lines changed 1, context: html, text, full: html, text
    renaming malacards.c to malaCards.c by email from Jim. Also changing the
    comments but not the table name, as it has already been pushed to the RR. no redmine.
    
• src/hg/hgGene/malaCards.c
  • lines changed 93, context: html, text, full: html, text
    renaming malacards.c to malaCards.c by email from Jim. Also changing the
    comments but not the table name, as it has already been pushed to the RR. no redmine.
    
• src/hg/hgGene/malacards.c
  • lines changed 97, context: html, text, full: html, text
    renaming malacards.c to malaCards.c by email from Jim. Also changing the
    comments but not the table name, as it has already been pushed to the RR. no redmine.
    
• src/hg/hgGene/mrnaDescriptions.c
  • lines changed 4, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
• src/hg/hgGene/pseudoGene.c
  • lines changed 3, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
• src/hg/hgGene/synonym.c
  • lines changed 3, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
• src/hg/hgSuggest/hgSuggest.c
  • lines changed 3, context: html, text, full: html, text
    hgSuggest (and most likely anything that needs to output JSON) needs to use jsonStringEscape instead of javaScriptLiteralEncode. Added cgiSpoof for command-line debugging.
    
  • lines changed 9, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
• src/hg/hgTables/hgTables.c
  • lines changed 3, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
• src/hg/hgTables/seqOut.c
  • lines changed 4, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 3, context: html, text, full: html, text
    How was this working ?
    
  • lines changed 17, context: html, text, full: html, text
    adding UI for refSeqComposite refs #13673
    
  • lines changed 4, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
  • lines changed 14, context: html, text, full: html, text
    protect omim button on refSeq UI refs #13673
    
• src/hg/hgTracks/cds.c
  • lines changed 6, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
• src/hg/hgTracks/gtexTracks.c
  • lines changed 10, context: html, text, full: html, text
    1. Load GTEx V6 data. Mods to tools and code to support multiple versions. 2. Use GTEx gene models rather than UCSC canonical
    
  • lines changed 13, context: html, text, full: html, text
    Fixing merge conflit
    
  • lines changed 2, context: html, text, full: html, text
    Load GTEx V6 gene table in hg19. refs #15645
    
  • lines changed 3, context: html, text, full: html, text
    Support for multiple GTEx releases/versions (to add V6 track). refs #15645
    
  • lines changed 9, context: html, text, full: html, text
    Add pseudogene transcript class (colored in dense mode. refs #15645
    
  • lines changed 4, context: html, text, full: html, text
    Adjust GTEx item height when filters are used. refs #15645
    
  • lines changed 5, context: html, text, full: html, text
    Minor cleanup. refs #15645
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
  • lines changed 2, context: html, text, full: html, text
    Fixing problem with custom-track bigDataUrl when cloning tracks across windows.
    
• src/hg/hgTracks/pslTrack.c
  • lines changed 4, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
• src/hg/hgTracks/retroGene.c
  • lines changed 3, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    fixup ncbiRef gene tracks to have the correct labels on the track longLabels refs #refs #13673
    
  • lines changed 25, context: html, text, full: html, text
    adding UI for refSeqComposite refs #13673
    
  • lines changed 19, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
  • lines changed 1, context: html, text, full: html, text
    removed no longer used implicity mapping of tracks named dless to dless.as type. This actually broke a track
    
  • lines changed 7, context: html, text, full: html, text
    manage the case of existing refGene track in new composite without the new tables refs #13673
    
  • lines changed 5, context: html, text, full: html, text
    Workaround for unexpected error: lookup of key [...] in sameItem hash failed
    
• src/hg/hgc/ccdsClick.c
  • lines changed 2, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
• src/hg/hgc/gtexClick.c
  • lines changed 209, context: html, text, full: html, text
    Tear out partial C implementation of gene expression boxplot. We will use R. refs #15645
    
  • lines changed 15, context: html, text, full: html, text
    Support for multiple GTEx releases/versions (to add V6 track). refs #15645
    
  • lines changed 1, context: html, text, full: html, text
    Remove debug statement
    
  • lines changed 5, context: html, text, full: html, text
    Query for transcript description in version agnostic way to accomodate changes to knownToEnsembl table (hg38 vs hg19)
    
  • lines changed 37, context: html, text, full: html, text
    Finishing touches to GTEx gene details page. Added link to hgGeneand bent knownGene queries for gene description to handle both hg38 and hg19 conventions. refs #15645
    
  • lines changed 31, context: html, text, full: html, text
    Suppress links to hgGene when there's no page. Add transcript class and color it. refs #15645
    
• src/hg/hgc/hgc.c
  • lines changed 54, context: html, text, full: html, text
    print out position links for ncbiRefSeq item refs #13673
    
  • lines changed 18, context: html, text, full: html, text
    ok to use showGenePos for ncbiRef tracks refs #refs #13673
    
  • lines changed 4, context: html, text, full: html, text
    ok to use showGenePos for ncbiRef tracks refs #refs #13673
    
  • lines changed 19, context: html, text, full: html, text
    need to make hte protein click links for the ncbiRefSeq resf #13673
    
  • lines changed 14, context: html, text, full: html, text
    code review clean up refs #16795
    
  • lines changed 80, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
• src/hg/hgc/hgcData/gtexBoxplot.R
  • lines changed 3, context: html, text, full: html, text
    Support for multiple GTEx releases/versions (to add V6 track). refs #15645
    
  • lines changed 3, context: html, text, full: html, text
    Widen boxplot a bit so longer sample count labels are readable.
    
• src/hg/hgc/mgcClick.c
  • lines changed 18, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
• src/hg/hgc/retroClick.c
  • lines changed 10, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 12, context: html, text, full: html, text
    Expanding BED FAQ via user suggestion, refs #124681
    
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 4, context: html, text, full: html, text
    Editing static pages to include micMur2 & ornAna2 refs #15098
    
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 3, context: html, text, full: html, text
    updating credits to include new ornAna2 assembly, refs #15098
    
  • lines changed 9, context: html, text, full: html, text
    Adding section for micMur2 to credits page, refs #15292
    
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 4, context: html, text, full: html, text
    Enhancing link per code review input on hub assembly quick start page refs #16781
    
• src/hg/htdocs/goldenPath/help/multiRegionHelp.html
  • lines changed 22, context: html, text, full: html, text
    Making session paths relative and adding notes about keyboard shortcuts to enter and exit multiregion, refs #16565
    
  • lines changed 5, context: html, text, full: html, text
    Fixing typo as per code review #16786
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 51, context: html, text, full: html, text
    Editing static pages to include micMur2 & ornAna2 refs #15098
    
  • lines changed 3, context: html, text, full: html, text
    Fixed release date from 2-9 to 2-10 & minor typo, refs #15098
    
  • lines changed 2, context: html, text, full: html, text
    Fixing minor typo, refs #15098
    
• src/hg/htdocs/indexNews.html
  • lines changed 96, context: html, text, full: html, text
    Editing static pages to include micMur2 & ornAna2 refs #15098
    
  • lines changed 2, context: html, text, full: html, text
    Fixed release date from 2-9 to 2-10 & minor typo, refs #15098
    
  • lines changed 5, context: html, text, full: html, text
    Fixing minor typo, refs #15098
    
  • lines changed 2, context: html, text, full: html, text
    Fixing minor typo, refs #15098
    
• src/hg/htdocs/training/index.html
  • lines changed 19, context: html, text, full: html, text
    dropping ref to completed workshop, adding ESHG, updating link to Kentucky
    
• src/hg/inc/genbank.h
  • lines changed 29, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
• src/hg/inc/gtexGeneBed.h
  • lines changed 3, context: html, text, full: html, text
    Support for multiple GTEx releases/versions (to add V6 track). refs #15645
    
• src/hg/inc/gtexInfo.h
  • lines changed 3, context: html, text, full: html, text
    Support for multiple GTEx releases/versions (to add V6 track). refs #15645
    
  • lines changed 4, context: html, text, full: html, text
    Make GTEx V6 the default. refs #16545
    
• src/hg/inc/gtexTranscript.h
  • lines changed 79, context: html, text, full: html, text
    Load GTEx V6 gene table in hg19. refs #15645
    
• src/hg/inc/gtexUi.h
  • lines changed 4, context: html, text, full: html, text
    Add JS to disable/enable GTEx gene track config controls when applicable. refs #15645
    
• src/hg/inc/hCommon.h
  • lines changed 3, context: html, text, full: html, text
    Finishing touches to GTEx gene details page. Added link to hgGeneand bent knownGene queries for gene description to handle both hg38 and hg19 conventions. refs #15645
    
• src/hg/js/hgTracks.js
  • lines changed 32, context: html, text, full: html, text
    Add apply button to trackUi popup (but suppress in description only page, e.g. from trtrackSearch results). refs #16788
    
• src/hg/js/utils.js
  • lines changed 1, context: html, text, full: html, text
    Disable (gray out) text label on codon numbering. Disabling the checkbox alone is non-obvious
    
  • lines changed 32, context: html, text, full: html, text
    Add JS to disable/enable GTEx gene track config controls when applicable. refs #15645
    
• src/hg/lib/genbank.c
  • lines changed 72, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
• src/hg/lib/geneGraph.c
  • lines changed 2, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
• src/hg/lib/gtexGeneBed.c
  • lines changed 9, context: html, text, full: html, text
    Support for multiple GTEx releases/versions (to add V6 track). refs #15645
    
  • lines changed 3, context: html, text, full: html, text
    Make GTEx V6 the default. refs #16545
    
• src/hg/lib/gtexInfo.c
  • lines changed 12, context: html, text, full: html, text
    Support for multiple GTEx releases/versions (to add V6 track). refs #15645
    
  • lines changed 18, context: html, text, full: html, text
    Make GTEx V6 the default. refs #16545
    
• src/hg/lib/gtexTranscript.as
  • lines changed 6, context: html, text, full: html, text
    Load GTEx V6 gene table in hg19. refs #15645
    
• src/hg/lib/gtexTranscript.c
  • lines changed 162, context: html, text, full: html, text
    Load GTEx V6 gene table in hg19. refs #15645
    
• src/hg/lib/gtexTranscript.sql
  • lines changed 12, context: html, text, full: html, text
    Load GTEx V6 gene table in hg19. refs #15645
    
• src/hg/lib/gtexUi.c
  • lines changed 1, context: html, text, full: html, text
    Fix problem with some tissue color patches on GTEx config pages. refs 15645
    
  • lines changed 45, context: html, text, full: html, text
    Add JS to disable/enable GTEx gene track config controls when applicable. refs #15645
    
  • lines changed 2, context: html, text, full: html, text
    Fix uninitialized cart var in GTEx ui. refs #15645
    
• src/hg/lib/hCommon.c
  • lines changed 7, context: html, text, full: html, text
    Finishing touches to GTEx gene details page. Added link to hgGeneand bent knownGene queries for gene description to handle both hg38 and hg19 conventions. refs #15645
    
• src/hg/lib/hdb.c
  • lines changed 11, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
  • lines changed 2, context: html, text, full: html, text
    allow for database.table format to be used in sqlGetField(). #16809
    
• src/hg/lib/hgFind.c
  • lines changed 40, context: html, text, full: html, text
    changes to allow for GenBank metadata to be held in a common table. #16809
    
• src/hg/lib/hui.c
  • lines changed 3, context: html, text, full: html, text
    Disable (gray out) text label on codon numbering. Disabling the checkbox alone is non-obvious
    
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Load GTEx V6 gene table in hg19. refs #15645
    
• src/hg/lib/ncbiRefSeqLink.as
  • lines changed 2, context: html, text, full: html, text
    correct spelling code review refs #16795
    
• src/hg/lib/ncbiRefSeqLink.sql
  • lines changed 2, context: html, text, full: html, text
    correct spelling code review refs #16795
    
• src/hg/makeDb/doc/gtex/2014-jan.txt
  • lines changed 2, context: html, text, full: html, text
    1. Load GTEx V6 data. Mods to tools and code to support multiple versions. 2. Use GTEx gene models rather than UCSC canonical
    
  • lines changed 218, context: html, text, full: html, text
    Load GTEx V6 gene table in hg19. refs #15645
    
• src/hg/makeDb/doc/gtex/V4.txt
  • lines changed 218, context: html, text, full: html, text
    Load GTEx V6 gene table in hg19. refs #15645
    
• src/hg/makeDb/doc/gtex/V6.txt
  • lines changed 68, context: html, text, full: html, text
    Load GTEx V6 gene table in hg19. refs #15645
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 15, context: html, text, full: html, text
    1. Load GTEx V6 data. Mods to tools and code to support multiple versions. 2. Use GTEx gene models rather than UCSC canonical
    
  • lines changed 21, context: html, text, full: html, text
    Load GTEx V6 gene table in hg19. refs #15645
    
• src/hg/makeDb/doc/hg38/gtex.txt
  • lines changed 24, context: html, text, full: html, text
    Update tools to load hg38.
    
• src/hg/makeDb/doc/mm10.txt
  • lines changed 56, context: html, text, full: html, text
    lastz chain net to rheMac8 refs #16744
    
• src/hg/makeDb/doc/rheMac2.txt
  • lines changed 17, context: html, text, full: html, text
    lift overs to rheMac8 refs #16744
    
• src/hg/makeDb/doc/rheMac3.txt
  • lines changed 19, context: html, text, full: html, text
    lift overs to rheMac8 refs #16744
    
• src/hg/makeDb/doc/rheMac8/initialBuild.txt
  • lines changed 357, context: html, text, full: html, text
    rheMac8 in the pushQ refs #16744
    
• src/hg/makeDb/doc/rheMac8/lastzRuns.txt
  • lines changed 51, context: html, text, full: html, text
    rheMac8 in the pushQ refs #16744
    
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added rheMac8 - Rhesus refs #16744
    
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    Added rheMac8 - Rhesus refs #16744
    
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 2, context: html, text, full: html, text
    turning on genbank updates for micMur2 on refs #15292
    
  • lines changed 2, context: html, text, full: html, text
    turning on rr genbank updates, refs #15098
    
• src/hg/makeDb/outside/hgGtex/hgGtex.c
  • lines changed 1, context: html, text, full: html, text
    1. Load GTEx V6 data. Mods to tools and code to support multiple versions. 2. Use GTEx gene models rather than UCSC canonical
    
  • lines changed 3, context: html, text, full: html, text
    Remove preliminary code for new GTEx feature (mean+whiskers on hgTracks) from build tool.
    
• src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed.c
  • lines changed 38, context: html, text, full: html, text
    1. Load GTEx V6 data. Mods to tools and code to support multiple versions. 2. Use GTEx gene models rather than UCSC canonical
    
  • lines changed 82, context: html, text, full: html, text
    Load GTEx V6 gene table in hg19. refs #15645
    
  • lines changed 93, context: html, text, full: html, text
    Update tools to load hg38.
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 9, context: html, text, full: html, text
    adding rheMac8 rules refs #16744
    
  • lines changed 22, context: html, text, full: html, text
    Add GTEx table keys. refs #15645
    
• src/hg/makeDb/trackDb/augustusGene.html
  • lines changed 1, context: html, text, full: html, text
    Track description page updates and changes for ce11, refs #15209
    
• src/hg/makeDb/trackDb/baboon/papAnu2/defaultPriority.ra
  • lines changed 13, context: html, text, full: html, text
    manage existing refGene tracks without the refSeqComposite refs #13673
    
• src/hg/makeDb/trackDb/baboon/papHam1/defaultPriority.ra
  • lines changed 13, context: html, text, full: html, text
    manage existing refGene tracks without the refSeqComposite refs #13673
    
• src/hg/makeDb/trackDb/bonobo/panPan1/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    manage existing refGene tracks without the refSeqComposite refs #13673
    
• src/hg/makeDb/trackDb/cat/felCat4/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    manage existing refGene tracks without the refSeqComposite refs #13673
    
• src/hg/makeDb/trackDb/cat/felCat5/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    manage existing refGene tracks without the refSeqComposite refs #13673
    
• src/hg/makeDb/trackDb/chainSelf.html
  • lines changed 4, context: html, text, full: html, text
    Track description page updates and changes for ce11, refs #15209
    
• src/hg/makeDb/trackDb/chicken/galGal4/trackDb.ra
  • lines changed 23, context: html, text, full: html, text
    manage existing refGene tracks without the refSeqComposite refs #13673
    
• src/hg/makeDb/trackDb/chimp/panTro1/defaultPriority.ra
  • lines changed 13, context: html, text, full: html, text
    manage existing refGene tracks without the refSeqComposite refs #13673
    
• src/hg/makeDb/trackDb/chimp/panTro2/defaultPriority.ra
  • lines changed 13, context: html, text, full: html, text
    manage existing refGene tracks without the refSeqComposite refs #13673
    
• src/hg/makeDb/trackDb/chimp/panTro3/defaultPriority.ra
  • lines changed 13, context: html, text, full: html, text
    manage existing refGene tracks without the refSeqComposite refs #13673
    
• src/hg/makeDb/trackDb/chimp/panTro4/defaultPriority.ra
  • lines changed 13, context: html, text, full: html, text
    manage existing refGene tracks without the refSeqComposite refs #13673
    
• src/hg/makeDb/trackDb/drosophila/dm2/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    manage existing refGene tracks without the refSeqComposite refs #13673
    
• src/hg/makeDb/trackDb/drosophila/dm6/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    manage existing refGene tracks without the refSeqComposite refs #13673
    
• src/hg/makeDb/trackDb/drosophila/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    manage existing refGene tracks without the refSeqComposite refs #13673
    
• src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    manage existing refGene tracks without the refSeqComposite refs #13673
    
• src/hg/makeDb/trackDb/horse/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    manage existing refGene tracks without the refSeqComposite refs #13673
    
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
  • lines changed 15, context: html, text, full: html, text
    adding rheMac8 chain net definitions refs #16744
    
  • lines changed 1, context: html, text, full: html, text
    adding rheMac8 chain net definitions refs #16744
    
• src/hg/makeDb/trackDb/human/chainNetRheMac3.ra
  • lines changed 15, context: html, text, full: html, text
    adding rheMac8 chain net definitions refs #16744
    
• src/hg/makeDb/trackDb/human/chainNetRheMac8.ra
  • lines changed 15, context: html, text, full: html, text
    adding rheMac8 chain net definitions refs #16744
    
• src/hg/makeDb/trackDb/human/gtexGeneExpr.html
  • lines changed 48, context: html, text, full: html, text
    Flesh out GTEx track description a bit, and update for V6. Thanks to Parisa for contributions refs #15645
    
• src/hg/makeDb/trackDb/human/hg16/defaultPriority.ra
  • lines changed 13, context: html, text, full: html, text
    manage existing refGene tracks without the refSeqComposite refs #13673
    
• src/hg/makeDb/trackDb/human/hg17/defaultPriority.ra
  • lines changed 13, context: html, text, full: html, text
    manage existing refGene tracks without the refSeqComposite refs #13673
    
• src/hg/makeDb/trackDb/human/hg18/defaultPriority.ra
  • lines changed 13, context: html, text, full: html, text
    manage existing refGene tracks without the refSeqComposite refs #13673
    
• src/hg/makeDb/trackDb/human/hg19/defaultPriority.ra
  • lines changed 13, context: html, text, full: html, text
    manage existing refGene tracks without the refSeqComposite refs #13673
    
• src/hg/makeDb/trackDb/human/hg19/gwipsvizRiboseq.html
  • lines changed 1, context: html, text, full: html, text
    Removed extra 'reads' from Description section; refs #16765
    
• src/hg/makeDb/trackDb/human/hg38/defaultPriority.ra
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• src/hg/makeDb/trackDb/human/hg38/gwipsvizRiboseq.html
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    Removed extra 'reads' from Description section; refs #16765
    
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
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    1. Load GTEx V6 data. Mods to tools and code to support multiple versions. 2. Use GTEx gene models rather than UCSC canonical
    
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    Flesh out GTEx track description a bit, and update for V6. Thanks to Parisa for contributions refs #15645
    
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    Make GTEx V6 the default. refs #16545
    
• src/hg/makeDb/trackDb/marmoset/calJac1/defaultPriority.ra
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    manage existing refGene tracks without the refSeqComposite refs #13673
    
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
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• src/hg/makeDb/trackDb/mouse/mm10/chainNetRheMac3.ra
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    adding rheMac8 chain net definitions refs #16744
    
• src/hg/makeDb/trackDb/mouse/mm10/chainNetRheMac8.ra
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    adding rheMac8 chain net definitions refs #16744
    
• src/hg/makeDb/trackDb/mouse/mm10/defaultPriority.ra
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• src/hg/makeDb/trackDb/mouse/mm10/trackDb.euarchontoglireChainNet.ra
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    adding rheMac8 chain net definitions refs #16744
    
• src/hg/makeDb/trackDb/mouse/mm7/defaultPriority.ra
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• src/hg/makeDb/trackDb/mouse/mm8/defaultPriority.ra
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• src/hg/makeDb/trackDb/mouse/mm9/defaultPriority.ra
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• src/hg/makeDb/trackDb/orangutan/ponAbe2/defaultPriority.ra
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• src/hg/makeDb/trackDb/pig/susScr3/trackDb.ra
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• src/hg/makeDb/trackDb/rabbit/oryCun2/trackDb.ra
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• src/hg/makeDb/trackDb/rat/rn3/defaultPriority.ra
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• src/hg/makeDb/trackDb/rat/rn4/defaultPriority.ra
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• src/hg/makeDb/trackDb/rat/rn5/defaultPriority.ra
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• src/hg/makeDb/trackDb/rat/rn6/defaultPriority.ra
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• src/hg/makeDb/trackDb/rat/trackDb.ra
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• src/hg/makeDb/trackDb/rhesus/rheMac2/defaultPriority.ra
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• src/hg/makeDb/trackDb/rhesus/rheMac3/defaultPriority.ra
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• src/hg/makeDb/trackDb/rhesus/rheMac8/description.html
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    add references to papers describing chrom naming schemes refs #16744
    
• src/hg/makeDb/trackDb/rhesus/rheMac8/trackDb.chainNet.ra
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    adding chain net overrides
    
• src/hg/makeDb/trackDb/rhesus/rheMac8/trackDb.ra
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    adding chain net overrides
    
• src/hg/makeDb/trackDb/squirt/ci1/trackDb.ra
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• src/hg/makeDb/trackDb/squirt/ci2/trackDb.ra
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• src/hg/makeDb/trackDb/squirt/cioSav2/trackDb.ra
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• src/hg/makeDb/trackDb/squirt/trackDb.ra
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• src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra
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    adding rheMac8 chain net definitions refs #16744
    
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
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    adding rheMac8 chain net definitions refs #16744
    
• src/hg/makeDb/trackDb/trackDb.ra
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    refGene in new composite needs to be release alpha refs #13673
    
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    cleaning up the ncbiRefSeq composite refs #13673
    
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    adding some searches for refSeqComposite refs #13673
    
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    code review fixups refs #16795
    
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    fixup search rules for refSeqComposite refs #13673
    
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    need release alpha in all stanzas to quite release beta make refs #13673
    
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    add pep table for ncbiRefSeq refs #13673
    
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    pepTable belongs on the PSL track refs #13673
    
• src/hg/makeDb/trackDb/worm/ce11/cons26way.html
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    Track description page updates and changes for ce11, refs #15209
    
• src/hg/makeDb/trackDb/worm/ce11/gap.html
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    Track description page updates and changes for ce11, refs #15209
    
• src/hg/makeDb/trackDb/worm/ce11/gold.html
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    Track description page updates and changes for ce11, refs #15209
    
• src/hg/makeDb/trackDb/worm/ce11/trackDb.ra
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• src/hg/makeDb/trackDb/worm/ce4/trackDb.ra
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• src/hg/makeDb/trackDb/worm/est.html
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    Track description page updates and changes for ce11, refs #15209
    
• src/hg/makeDb/trackDb/worm/intronEst.html
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    Track description page updates and changes for ce11, refs #15209
    
• src/hg/makeDb/trackDb/worm/mrna.html
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    Track description page updates and changes for ce11, refs #15209
    
• src/hg/makeDb/trackDb/worm/refGene.html
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    Track description page updates and changes for ce11, refs #15209
    
• src/hg/makeDb/trackDb/worm/trackDb.ra
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• src/hg/makeDb/trackDb/worm/ws245Genes.html
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    Track description page updates and changes for ce11, refs #15209
    
• src/hg/makeDb/trackDb/worm/xenoMrna.html
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    Track description page updates and changes for ce11, refs #15209
    
• src/hg/makeDb/trackDb/zebrafish/danRer10/trackDb.ra
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    manage existing refGene tracks without the refSeqComposite refs #13673
    
• src/hg/utils/hubCrawl/hubCrawl.c
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    hubCrawl now includes genomes.txt fields organism, description and scientificName (if provided).
    Previously, searching for "arabidopsis" did not bring up the DNA Methylation hub because its
    description html has an img that shows arabidopsis counts, but no "arabidopsis" in the text.
    
• src/hg/utils/otto/lovd/checkAndLoad.sh
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    fixed bug in the LOVD otto script, Matt realized it wasn't working
    anymore, no redmine
    
• src/hg/utils/otto/omim/buildOmimTracks.csh
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    Initial commit of updated OMIM pipeline, refs #14465
    
• src/hg/utils/otto/omim/checkOmim.sh
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    Initial commit of updated OMIM pipeline, refs #14465
    
• src/hg/utils/otto/omim/checkOmimUpload.sh
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    Initial commit of updated OMIM pipeline, refs #14465
    
• src/hg/utils/otto/omim/doOmimPhenotype.pl
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    Initial commit of updated OMIM pipeline, refs #14465
    
• src/inc/cheapcgi.h
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    Add JS to disable/enable GTEx gene track config controls when applicable. refs #15645
    
• src/lib/bamFile.c
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    assume BAM index is in fileName.bai #16800
    
• src/lib/cheapcgi.c
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    Add JS to disable/enable GTEx gene track config controls when applicable. refs #15645
    
• src/utils/qa/weeklybld/buildEnv.csh
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    v329 preview1 refs #16669
    
• src/utils/qa/weeklybld/sendLogEmail.pl
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    fixup correct From: and Cc: email addresses refs #16802
    

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