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 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 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 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
- lines changed 14, context: html, text, full: html, text
manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/human/hg38/gwipsvizRiboseq.html
- lines changed 1, context: html, text, full: html, text
Removed extra 'reads' from Description section; refs #16765
- src/hg/makeDb/trackDb/human/trackDb.gtex.ra
- lines changed 9, 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 2, context: html, text, full: html, text
Flesh out GTEx track description a bit, and update for V6. Thanks to Parisa for contributions refs #15645
- lines changed 5, context: html, text, full: html, text
Make GTEx V6 the default. refs #16545
- src/hg/makeDb/trackDb/marmoset/calJac1/defaultPriority.ra
- lines changed 13, context: html, text, full: html, text
manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
- lines changed 13, context: html, text, full: html, text
manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/mouse/mm10/chainNetRheMac3.ra
- lines changed 15, context: html, text, full: html, text
adding rheMac8 chain net definitions refs #16744
- src/hg/makeDb/trackDb/mouse/mm10/chainNetRheMac8.ra
- lines changed 15, context: html, text, full: html, text
adding rheMac8 chain net definitions refs #16744
- src/hg/makeDb/trackDb/mouse/mm10/defaultPriority.ra
- lines changed 13, context: html, text, full: html, text
manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.euarchontoglireChainNet.ra
- lines changed 15, context: html, text, full: html, text
adding rheMac8 chain net definitions refs #16744
- src/hg/makeDb/trackDb/mouse/mm7/defaultPriority.ra
- lines changed 13, context: html, text, full: html, text
manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/mouse/mm8/defaultPriority.ra
- lines changed 13, context: html, text, full: html, text
manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/mouse/mm9/defaultPriority.ra
- lines changed 13, context: html, text, full: html, text
manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/orangutan/ponAbe2/defaultPriority.ra
- lines changed 13, context: html, text, full: html, text
manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/pig/susScr3/trackDb.ra
- lines changed 13, context: html, text, full: html, text
manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/rabbit/oryCun2/trackDb.ra
- lines changed 13, context: html, text, full: html, text
manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/rat/rn3/defaultPriority.ra
- lines changed 13, context: html, text, full: html, text
manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/rat/rn4/defaultPriority.ra
- lines changed 13, context: html, text, full: html, text
manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/rat/rn5/defaultPriority.ra
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manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/rat/rn6/defaultPriority.ra
- lines changed 13, context: html, text, full: html, text
manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/rat/trackDb.ra
- lines changed 13, context: html, text, full: html, text
manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/rhesus/rheMac2/defaultPriority.ra
- lines changed 14, context: html, text, full: html, text
manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/rhesus/rheMac3/defaultPriority.ra
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manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/rhesus/rheMac8/description.html
- lines changed 50, context: html, text, full: html, text
add references to papers describing chrom naming schemes refs #16744
- src/hg/makeDb/trackDb/rhesus/rheMac8/trackDb.chainNet.ra
- lines changed 14, context: html, text, full: html, text
adding chain net overrides
- src/hg/makeDb/trackDb/rhesus/rheMac8/trackDb.ra
- lines changed 8, context: html, text, full: html, text
adding chain net overrides
- src/hg/makeDb/trackDb/squirt/ci1/trackDb.ra
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manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/squirt/ci2/trackDb.ra
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manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/squirt/cioSav2/trackDb.ra
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manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/squirt/trackDb.ra
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manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra
- lines changed 212, context: html, text, full: html, text
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
- lines changed 1, context: html, text, full: html, text
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
- lines changed 13, context: html, text, full: html, text
fixup search rules for refSeqComposite refs #13673
- lines changed 7, context: html, text, full: html, text
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
- lines changed 80, context: html, text, full: html, text
Track description page updates and changes for ce11, refs #15209
- src/hg/makeDb/trackDb/worm/ce11/gap.html
- lines changed 2, context: html, text, full: html, text
Track description page updates and changes for ce11, refs #15209
- src/hg/makeDb/trackDb/worm/ce11/gold.html
- lines changed 2, context: html, text, full: html, text
Track description page updates and changes for ce11, refs #15209
- src/hg/makeDb/trackDb/worm/ce11/trackDb.ra
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manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/worm/ce4/trackDb.ra
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manage existing refGene tracks without the refSeqComposite refs #13673
- src/hg/makeDb/trackDb/worm/est.html
- lines changed 13, context: html, text, full: html, text
Track description page updates and changes for ce11, refs #15209
- src/hg/makeDb/trackDb/worm/intronEst.html
- lines changed 13, context: html, text, full: html, text
Track description page updates and changes for ce11, refs #15209
- src/hg/makeDb/trackDb/worm/mrna.html
- lines changed 12, context: html, text, full: html, text
Track description page updates and changes for ce11, refs #15209
- src/hg/makeDb/trackDb/worm/refGene.html
- lines changed 15, context: html, text, full: html, text
Track description page updates and changes for ce11, refs #15209
- src/hg/makeDb/trackDb/worm/trackDb.ra
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manage existing refGene tracks without the refSeqComposite refs #13673
- 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
- lines changed 16, context: html, text, full: html, text
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
- lines changed 3, context: html, text, full: html, text
fixed bug in the LOVD otto script, Matt realized it wasn't working
anymore, no redmine
- src/hg/utils/otto/omim/buildOmimTracks.csh
- lines changed 112, context: html, text, full: html, text
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
- lines changed 22, context: html, text, full: html, text
Initial commit of updated OMIM pipeline, refs #14465
- src/hg/utils/otto/omim/doOmimPhenotype.pl
- lines changed 95, context: html, text, full: html, text
Initial commit of updated OMIM pipeline, refs #14465
- src/inc/cheapcgi.h
- lines changed 3, context: html, text, full: html, text
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
- lines changed 9, context: html, text, full: html, text
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
- lines changed 2, context: html, text, full: html, text
fixup correct From: and Cc: email addresses refs #16802
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- files changed: 214