Commits for kate
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v328_base to v329_preview (2016-02-08 to 2016-02-15) v329
- 1. Load GTEx V6 data. Mods to tools and code to support multiple versions. 2. Use GTEx gene models rather than UCSC canonical
- src/hg/hgTracks/gtexTracks.c - lines changed 10, context: html, text, full: html, text
- src/hg/makeDb/doc/gtex/2014-jan.txt - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/doc/hg19.txt - lines changed 15, context: html, text, full: html, text
- src/hg/makeDb/outside/hgGtex/hgGtex.c - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed.c - lines changed 38, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.gtex.ra - lines changed 9, context: html, text, full: html, text
- Fixing merge conflit
- src/hg/hgTracks/gtexTracks.c - lines changed 13, context: html, text, full: html, text
- Load GTEx V6 gene table in hg19. refs #15645
- src/hg/hgTracks/gtexTracks.c - lines changed 2, context: html, text, full: html, text
- src/hg/inc/gtexTranscript.h - lines changed 79, context: html, text, full: html, text
- src/hg/lib/gtexTranscript.as - lines changed 6, context: html, text, full: html, text
- src/hg/lib/gtexTranscript.c - lines changed 162, context: html, text, full: html, text
- src/hg/lib/gtexTranscript.sql - lines changed 12, context: html, text, full: html, text
- src/hg/makeDb/doc/gtex/2014-jan.txt - lines changed 218, context: html, text, full: html, text
- src/hg/makeDb/doc/gtex/V4.txt - lines changed 218, context: html, text, full: html, text
- src/hg/makeDb/doc/gtex/V6.txt - lines changed 68, context: html, text, full: html, text
- src/hg/makeDb/doc/hg19.txt - lines changed 21, context: html, text, full: html, text
- src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed.c - lines changed 82, context: html, text, full: html, text
- Update tools to load hg38.
- src/hg/makeDb/doc/hg38/gtex.txt - lines changed 24, context: html, text, full: html, text
- src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed.c - lines changed 93, context: html, text, full: html, text
- How was this working ?
- src/hg/hgTrackUi/hgTrackUi.c - lines changed 3, 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
- Fix problem with some tissue color patches on GTEx config pages. refs 15645
- Disable (gray out) text label on codon numbering. Disabling the checkbox alone is non-obvious
- Add JS to disable/enable GTEx gene track config controls when applicable. refs #15645
- Tear out partial C implementation of gene expression boxplot. We will use R. refs #15645
- src/hg/hgc/gtexClick.c - lines changed 209, context: html, text, full: html, text
- Merge branch 'gtexHgc'
- Merge branch 'master' into gtex6
- Support for multiple GTEx releases/versions (to add V6 track). refs #15645
- src/hg/hgTracks/gtexTracks.c - lines changed 3, context: html, text, full: html, text
- src/hg/hgc/hgcData/gtexBoxplot.R - lines changed 3, context: html, text, full: html, text
- src/hg/inc/gtexGeneBed.h - lines changed 3, context: html, text, full: html, text
- 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
- src/hg/hgc/gtexClick.c - lines changed 15, context: html, text, full: html, text
- Remove debug statement
- Widen boxplot a bit so longer sample count labels are readable.
- src/hg/hgc/hgcData/gtexBoxplot.R - lines changed 3, context: html, text, full: html, text
- Query for transcript description in version agnostic way to accomodate changes to knownToEnsembl table (hg38 vs hg19)
- 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/hgc/gtexClick.c - lines changed 37, context: html, text, full: html, text
- Add pseudogene transcript class (colored in dense mode. refs #15645
- src/hg/hgTracks/gtexTracks.c - lines changed 9, 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/gtexClick.c - lines changed 31, context: html, text, full: html, text
- Merge branch 'gtex6'
- Adjust GTEx item height when filters are used. refs #15645
- src/hg/hgTracks/gtexTracks.c - lines changed 4, context: html, text, full: html, text
- Minor cleanup. refs #15645
- src/hg/hgTracks/gtexTracks.c - lines changed 5, 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/gtexGeneExpr.html - lines changed 48, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.gtex.ra - lines changed 2, context: html, text, full: html, text
- Make GTEx V6 the default. refs #16545
- src/hg/lib/gtexGeneBed.c - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.gtex.ra - lines changed 5, context: html, text, full: html, text
- Merge branch 'gtex6'
- Add GTEx table keys. refs #15645
- src/hg/makeDb/schema/all.joiner - lines changed 22, context: html, text, full: html, text
- Remove preliminary code for new GTEx feature (mean+whiskers on hgTracks) from build tool.
- src/hg/makeDb/outside/hgGtex/hgGtex.c - lines changed 3, context: html, text, full: html, text
- Fix uninitialized cart var in GTEx ui. refs #15645
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