CVS changes by file
branch to review (2010-01-19 to 2010-01-26) v224
- src/hg/archaeStuff/data/Genome-info-mods
- 1.95 lines changed: 4, context: html, text, full: html, text
- 1.94 lines changed: 2, context: html, text, full: html, text
fix Pyrobaculum genome ordering
- 1.93 lines changed: 50, context: html, text, full: html, text
changed T. neutrophilus to Pyrobaculum by Todd; add Francisella genomes
- src/hg/archaeStuff/scripts/archaeBrowser/CRISPR.pm
- 1.3 lines changed: 15, context: html, text, full: html, text
fix code in parsing CRT output
- 1.2 lines changed: 7, context: html, text, full: html, text
load precomputed crispr with tab option
- 1.1 lines changed: 22, context: html, text, full: html, text
add CRISPR track
- src/hg/archaeStuff/scripts/make-browser-2.0
- src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
- 1.24 lines changed: 2, context: html, text, full: html, text
Insignificant change. This is not hgEncodeDownloads.pl
- 1.23 lines changed: 18, context: html, text, full: html, text
1. Add checksum option 2. Add plain text version of index file 3. Fix file perms
- src/hg/encode/encodeValidate/config/cv.ra
- 1.200 lines changed: 1, context: html, text, full: html, text
pravastatin treatment illucidated by Yale
- 1.199 lines changed: 7, context: html, text, full: html, text
Adde pravastatin treatment and renamed SREBP1A to SREBP1 for Yale
- 1.198 lines changed: 5, context: html, text, full: html, text
Some metadata corrections for Yale
- src/hg/encode/encodeValidate/doEncodeReport.pl
- 1.11 lines changed: 25, context: html, text, full: html, text
Now using submission ID from trackDb to lookup status in projects table, instead of relying on matching metadata. This version only includes latest version (e.g. V2 if any) of experiments
- 1.10 lines changed: 4, context: html, text, full: html, text
Revert to non-debug version
- src/hg/encode/hgEncodeSubmit/app/views/pipeline/show.rhtml
- 1.52 lines changed: 109, context: html, text, full: html, text
doing a little lookahead, storing results in boolean vars, eliminating redundancy
- src/hg/hgTables/mainPage.c
- 1.146 lines changed: 1, context: html, text, full: html, text
Clarified ENCODE regions label (thanks Kayla/Ann).
- src/hg/hgTrackUi/hgTrackUi.c
- 1.514 lines changed: 15, context: html, text, full: html, text
Microarray tracks and custom microarray tracks now support the "expColor" trackDb setting which can be "redGreen" (default), "redBlue", "redBlueOnWhite", "yellowBlue", or "redBlueOnYellow". Some things wre changed around so that adding more color options in the future is a cinch.
- src/hg/hgTracks/bigBedTrack.c
- 1.3 lines changed: 6, context: html, text, full: html, text
Getting rid of special case to allow filtering of bigBed in dense mode.
- src/hg/hgTracks/expRatioTracks.c
- 1.48 lines changed: 47, context: html, text, full: html, text
Microarray tracks and custom microarray tracks now support the "expColor" trackDb setting which can be "redGreen" (default), "redBlue", "redBlueOnWhite", "yellowBlue", or "redBlueOnYellow". Some things wre changed around so that adding more color options in the future is a cinch.
- src/hg/hgTracks/hgTracks.h
- 1.198 lines changed: 6, context: html, text, full: html, text
Microarray tracks and custom microarray tracks now support the "expColor" trackDb setting which can be "redGreen" (default), "redBlue", "redBlueOnWhite", "yellowBlue", or "redBlueOnYellow". Some things wre changed around so that adding more color options in the future is a cinch.
- src/hg/hgTracks/simpleTracks.c
- 1.122 lines changed: 16, context: html, text, full: html, text
Microarray tracks and custom microarray tracks now support the "expColor" trackDb setting which can be "redGreen" (default), "redBlue", "redBlueOnWhite", "yellowBlue", or "redBlueOnYellow". Some things wre changed around so that adding more color options in the future is a cinch.
- src/hg/hgc/expClick.c
- 1.24 lines changed: 65, context: html, text, full: html, text
Microarray tracks and custom microarray tracks now support the "expColor" trackDb setting which can be "redGreen" (default), "redBlue", "redBlueOnWhite", "yellowBlue", or "redBlueOnYellow". Some things wre changed around so that adding more color options in the future is a cinch.
- src/hg/hgc/hgc.c
- 1.1594 lines changed: 1, context: html, text, full: html, text
Updated one line for tRNAs details page.
- 1.1593 lines changed: 7, context: html, text, full: html, text
Updated tRNAs track processing per input from Mark and Todd.
- 1.1592 lines changed: 8, context: html, text, full: html, text
pgSjk was not hooked up to doPgSnp, oops! Tweaked wording in pgSnp.
- 1.1591 lines changed: 96, context: html, text, full: html, text
gwasCatalog: Added links to dbSNP for snp and, if different, the snp with the risk allele. Look up and display the dbSNP observed alleles, and warn if they are complementary (then the risk allele is ambiguous because strand is not noted.
- 1.1590 lines changed: 26, context: html, text, full: html, text
For snp125+, if there is a gwasCatalog table that also contains the SNP, make a link to open the track in hgTracks (like we do for HapMap).
- 1.1589 lines changed: 68, context: html, text, full: html, text
Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies).
- src/hg/inc/gwasCatalog.h
- 1.1 lines changed: 0, context: html, text, full: html, text
Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies).
- src/hg/inc/microarray.h
- 1.11 lines changed: 13, context: html, text, full: html, text
Microarray tracks and custom microarray tracks now support the "expColor" trackDb setting which can be "redGreen" (default), "redBlue", "redBlueOnWhite", "yellowBlue", or "redBlueOnYellow". Some things wre changed around so that adding more color options in the future is a cinch.
- src/hg/instinct/hgGeneset/bioIntDb.c
- 1.1 lines changed: 0, context: html, text, full: html, text
Adding new geneset binaries to cvs
- src/hg/instinct/hgGeneset/bioIntDb.h
- 1.1 lines changed: 0, context: html, text, full: html, text
Adding new geneset binaries to cvs
- src/hg/instinct/hgGeneset/bioIntDriver.c
- 1.1 lines changed: 0, context: html, text, full: html, text
Adding new geneset binaries to cvs
- src/hg/instinct/hgGeneset/bioIntDriver.h
- 1.2 lines changed: 1, context: html, text, full: html, text
added initial drawing code
- 1.1 lines changed: 1, context: html, text, full: html, text
Adding new geneset binaries to cvs
- src/hg/instinct/hgGeneset/createTables.c
- 1.1 lines changed: 0, context: html, text, full: html, text
Adding new geneset binaries to cvs
- src/hg/instinct/hgGeneset/drawingCode.c
- 1.2 lines changed: 75, context: html, text, full: html, text
updated drawing code
- 1.1 lines changed: 75, context: html, text, full: html, text
added initial drawing code
- src/hg/instinct/hgGeneset/frontend/css/hgHeatmapStyle.css
- 1.1 lines changed: 0, context: html, text, full: html, text
Whoops, forgot frontend
- src/hg/instinct/hgGeneset/frontend/css/jquery-ui-1.7.1.css
- 1.1 lines changed: 0, context: html, text, full: html, text
Whoops, forgot frontend
- src/hg/instinct/hgGeneset/frontend/genesetView.html
- 1.1 lines changed: 0, context: html, text, full: html, text
Whoops, forgot frontend
- src/hg/instinct/hgGeneset/frontend/index.html
- 1.1 lines changed: 0, context: html, text, full: html, text
Whoops, forgot frontend
- src/hg/instinct/hgGeneset/frontend/js/hgHeatmapGeneset.js
- 1.1 lines changed: 0, context: html, text, full: html, text
Whoops, forgot frontend
- src/hg/instinct/hgGeneset/frontend/js/jquery-1.3.2.js
- 1.1 lines changed: 0, context: html, text, full: html, text
Whoops, forgot frontend
- src/hg/instinct/hgGeneset/frontend/js/jquery-ui-1.7.1.min.js
- 1.1 lines changed: 0, context: html, text, full: html, text
Whoops, forgot frontend
- src/hg/instinct/hgGeneset/hgGenesets.c
- 1.4 lines changed: 48, context: html, text, full: html, text
updated drawing code
- 1.3 lines changed: 379, context: html, text, full: html, text
added initial drawing code
- 1.2 lines changed: 1, context: html, text, full: html, text
Whoops, forgot frontend
- 1.1 lines changed: 400, context: html, text, full: html, text
Adding new geneset binaries to cvs
- src/hg/instinct/hgGeneset/hgGenesets.h
- 1.3 lines changed: 28, context: html, text, full: html, text
updated drawing code
- 1.2 lines changed: 45, context: html, text, full: html, text
added initial drawing code
- 1.1 lines changed: 62, context: html, text, full: html, text
Adding new geneset binaries to cvs
- src/hg/instinct/hgGeneset/makefile
- 1.2 lines changed: 1, context: html, text, full: html, text
added initial drawing code
- 1.1 lines changed: 1, context: html, text, full: html, text
Adding new geneset binaries to cvs
- src/hg/instinct/hgGeneset/populateDb.c
- 1.1 lines changed: 0, context: html, text, full: html, text
Adding new geneset binaries to cvs
- src/hg/instinct/hgGeneset/trashDirMD5.c
- 1.1 lines changed: 0, context: html, text, full: html, text
added initial drawing code
- src/hg/lib/customFactory.c
- 1.114 lines changed: 1, context: html, text, full: html, text
Added verbose4 message to add customTrash db tables to the output used by the refresh script.
- src/hg/lib/gwasCatalog.as
- 1.1 lines changed: 0, context: html, text, full: html, text
Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies).
- src/hg/lib/gwasCatalog.c
- 1.1 lines changed: 0, context: html, text, full: html, text
Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies).
- src/hg/lib/gwasCatalog.sql
- 1.1 lines changed: 0, context: html, text, full: html, text
Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies).
- src/hg/lib/hui.c
- 1.254 lines changed: 1, context: html, text, full: html, text
baseColorDrawOptDropDown: Similarly to the drop-down labels, use 'base' not 'mRNA' in help link label when there is no coding info.
- src/hg/lib/makefile
- 1.400 lines changed: 1, context: html, text, full: html, text
Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies).
- src/hg/lib/microarray.c
- 1.11 lines changed: 14, context: html, text, full: html, text
Microarray tracks and custom microarray tracks now support the "expColor" trackDb setting which can be "redGreen" (default), "redBlue", "redBlueOnWhite", "yellowBlue", or "redBlueOnYellow". Some things wre changed around so that adding more color options in the future is a cinch.
- src/hg/lib/pgSnp.c
- 1.7 lines changed: 5, context: html, text, full: html, text
Tweaked label of coding changes. If there are no coding changes, suppress messages about coding changes (confused me a bit).
- src/hg/lib/trackDbCustom.c
- 1.74 lines changed: 1, context: html, text, full: html, text
Removing score filter from bigBed.
- src/hg/makeDb/doc/ailMel1.txt
- 1.3 lines changed: 54, context: html, text, full: html, text
genbank done for ailMel1
- src/hg/makeDb/doc/aplCal1.txt
- 1.10 lines changed: 3, context: html, text, full: html, text
disable aplCal1 refseqs, since there are none
- src/hg/makeDb/doc/bosTau4.txt
- 1.22 lines changed: 61, context: html, text, full: html, text
panda aligned to dog,rat,mouse,human,opossum pig aligned to mouse,human,opossum,cow bosTau4 to rn4, rabbit to rat,mouse,opossum,guineaPig
- src/hg/makeDb/doc/canFam2.txt
- 1.26 lines changed: 63, context: html, text, full: html, text
panda aligned to dog,rat,mouse,human,opossum pig aligned to mouse,human,opossum,cow bosTau4 to rn4, rabbit to rat,mouse,opossum,guineaPig
- src/hg/makeDb/doc/encodeDccHg18/broadBernstein.txt
- 1.11 lines changed: 213, context: html, text, full: html, text
Older stuff and Jan 2010 freeze notes
- src/hg/makeDb/doc/encodeDccHg18/broadChipSeq.notes.txt
- src/hg/makeDb/doc/encodeDccHg18/dukeUtaUncCrawford.txt
- 1.11 lines changed: 176, context: html, text, full: html, text
Older stuff and Jan 2010 freeze notes
- src/hg/makeDb/doc/encodeDccHg18/uwStam.txt
- 1.6 lines changed: 715, context: html, text, full: html, text
Older stuff and Jan 2010 freeze notes
- src/hg/makeDb/doc/encodeDccHg18/yaleDavisHarvardSnyder.txt
- 1.14 lines changed: 850, context: html, text, full: html, text
Jan 2010 freeze notes
- src/hg/makeDb/doc/hg18.txt
- 1.395 lines changed: 47, context: html, text, full: html, text
Adding a mapability data from CRG.
- src/hg/makeDb/doc/hg19.txt
- 1.75 lines changed: 40, context: html, text, full: html, text
Adding a mapability data from CRG.
- 1.74 lines changed: 104, context: html, text, full: html, text
panda aligned to dog,rat,mouse,human,opossum pig aligned to mouse,human,opossum,cow bosTau4 to rn4, rabbit to rat,mouse,opossum,guineaPig
- 1.73 lines changed: 9, context: html, text, full: html, text
Added template for Genome Variants (pgSnp) liftOver from hg18 by Belinda.
- 1.72 lines changed: 18, context: html, text, full: html, text
Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies).
- src/hg/makeDb/doc/mm9.txt
- 1.121 lines changed: 177, context: html, text, full: html, text
panda aligned to dog,rat,mouse,human,opossum pig aligned to mouse,human,opossum,cow bosTau4 to rn4, rabbit to rat,mouse,opossum,guineaPig
- src/hg/makeDb/doc/monDom5.txt
- 1.17 lines changed: 94, context: html, text, full: html, text
panda aligned to dog,rat,mouse,human,opossum pig aligned to mouse,human,opossum,cow bosTau4 to rn4, rabbit to rat,mouse,opossum,guineaPig
- src/hg/makeDb/doc/oryCun1.txt
- 1.10 lines changed: 33, context: html, text, full: html, text
liftOver done to oryCun2
- src/hg/makeDb/doc/oryCun2.txt
- 1.5 lines changed: 100, context: html, text, full: html, text
panda aligned to dog,rat,mouse,human,opossum pig aligned to mouse,human,opossum,cow bosTau4 to rn4, rabbit to rat,mouse,opossum,guineaPig
- src/hg/makeDb/doc/rn4.txt
- 1.36 lines changed: 112, context: html, text, full: html, text
panda aligned to dog,rat,mouse,human,opossum pig aligned to mouse,human,opossum,cow bosTau4 to rn4, rabbit to rat,mouse,opossum,guineaPig
- src/hg/makeDb/doc/susScr1.txt
- 1.4 lines changed: 48, context: html, text, full: html, text
panda aligned to dog,rat,mouse,human,opossum pig aligned to mouse,human,opossum,cow bosTau4 to rn4, rabbit to rat,mouse,opossum,guineaPig
- src/hg/makeDb/genbank/etc/align.dbs
- 1.108 lines changed: 1, context: html, text, full: html, text
Adding ailMel1 - Panda - Ailuropoda melanoleuca
- src/hg/makeDb/genbank/etc/genbank.conf
- 1.359 lines changed: 1, context: html, text, full: html, text
no lift file is required for panda
- 1.358 lines changed: 1, context: html, text, full: html, text
disable aplCal1 refseqs, since there are none
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- 1.112 lines changed: 1, context: html, text, full: html, text
Adding ailMel1 - Panda - Ailuropoda melanoleuca
- src/hg/makeDb/schema/all.joiner
- 1.767 lines changed: 16, context: html, text, full: html, text
adding definitions for oryCun2
- 1.766 lines changed: 3, context: html, text, full: html, text
Added gwasCatalog.
- src/hg/makeDb/trackDb/README
- 1.98 lines changed: 2, context: html, text, full: html, text
Added to expRatio spec the "expColor" trackDb setting.
- 1.97 lines changed: 17, context: html, text, full: html, text
Added 'type bam' description.
- src/hg/makeDb/trackDb/all_est.html
- 1.13 lines changed: 1, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/all_mrna.html
- 1.11 lines changed: 1, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/anopheles/est.html
- 1.5 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/anopheles/intronEst.html
- 1.7 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/anopheles/mrna.html
- 1.5 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/anopheles/xenoMrna.html
- 1.5 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/apis/all_est.html
- 1.6 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/apis/all_mrna.html
- 1.7 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/apis/intronEst.html
- 1.7 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/apis/xenoMrna.html
- 1.5 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/chicken/galGal2/trackDb.ra
- 1.75 lines changed: 28, context: html, text, full: html, text
moved all panTro2 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/chicken/galGal3/trackDb.chainNet.ra
- 1.2 lines changed: 3, context: html, text, full: html, text
Switching equCab1 and equCab2 chains and nets to composites. EquCab1 is currently on RR for hg18, mm8, panTro2 and rn4. EquCab1 is on RR for canFam2, galGal3, hg19, mm9, monDom5, ornaAna1.
- src/hg/makeDb/trackDb/chicken/galGal3/trackDb.ra
- 1.19 lines changed: 6, context: html, text, full: html, text
Changing opossum net and chain tracks to composites. The following assemblies are currently live on the RR: calJac1 canFam2 cavPor3 danRer4 danRer5 galGal2 galGal3 hg17 hg18 hg19 mm8 mm9 ornAna1 panTro2 ponAbe2 rheMac2 rn4 xenTro2.
- src/hg/makeDb/trackDb/chicken/trackDb.ra
- 1.18 lines changed: 8, context: html, text, full: html, text
Switching equCab1 and equCab2 chains and nets to composites. EquCab1 is currently on RR for hg18, mm8, panTro2 and rn4. EquCab1 is on RR for canFam2, galGal3, hg19, mm9, monDom5, ornaAna1.
- src/hg/makeDb/trackDb/chimp/panTro2/est.html
- 1.3 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/chimp/panTro2/intronEst.html
- 1.5 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/chimp/panTro2/mrna.html
- 1.3 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
- 1.50 lines changed: 8, context: html, text, full: html, text
Changing opossum net and chain tracks to composites. The following assemblies are currently live on the RR: calJac1 canFam2 cavPor3 danRer4 danRer5 galGal2 galGal3 hg17 hg18 hg19 mm8 mm9 ornAna1 panTro2 ponAbe2 rheMac2 rn4 xenTro2.
- 1.49 lines changed: 3, context: html, text, full: html, text
moved all galGal22 chains and nets to composite and dropped individual tracks
- 1.48 lines changed: 4, context: html, text, full: html, text
moved all rheMac2 chains and nets to composite and dropped individual tracks
- 1.47 lines changed: 0, context: html, text, full: html, text
moved all calJac1 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/chimp/panTro2/xenoMrna.html
- 1.4 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/chimp/trackDb.ra
- 1.29 lines changed: 26, context: html, text, full: html, text
moved all rheMac2 chains and nets to composite and dropped individual tracks
- 1.28 lines changed: 3, context: html, text, full: html, text
moved all calJac1 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/dog/canFam2/trackDb.chainNet.ra
- 1.3 lines changed: 4, context: html, text, full: html, text
Switching equCab1 and equCab2 chains and nets to composites. EquCab1 is currently on RR for hg18, mm8, panTro2 and rn4. EquCab1 is on RR for canFam2, galGal3, hg19, mm9, monDom5, ornaAna1.
- src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
- 1.47 lines changed: 6, context: html, text, full: html, text
Changing opossum net and chain tracks to composites. The following assemblies are currently live on the RR: calJac1 canFam2 cavPor3 danRer4 danRer5 galGal2 galGal3 hg17 hg18 hg19 mm8 mm9 ornAna1 panTro2 ponAbe2 rheMac2 rn4 xenTro2.
- 1.46 lines changed: 7, context: html, text, full: html, text
moved all panTro2 chains and nets to composite and dropped individual tracks
- 1.45 lines changed: 6, context: html, text, full: html, text
moved all calJac1 chains and nets to composite and dropped individual tracks
- 1.44 lines changed: 6, context: html, text, full: html, text
Switched all chainFelCat3 and netFelCat3 tracks to be composite chainNetFelCat3 tracks.
- src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra
- 1.13 lines changed: 3, context: html, text, full: html, text
adding Panda and Pig chainNet composite tracks
- src/hg/makeDb/trackDb/dog/trackDb.ra
- 1.37 lines changed: 8, context: html, text, full: html, text
moved all rheMac2 chains and nets to composite and dropped individual tracks
- 1.36 lines changed: 6, context: html, text, full: html, text
moved all panTro2 chains and nets to composite and dropped individual tracks
- 1.35 lines changed: 28, context: html, text, full: html, text
Switching equCab1 and equCab2 chains and nets to composites. EquCab1 is currently on RR for hg18, mm8, panTro2 and rn4. EquCab1 is on RR for canFam2, galGal3, hg19, mm9, monDom5, ornaAna1.
- 1.34 lines changed: 7, context: html, text, full: html, text
moved all calJac1 chains and nets to composite and dropped individual tracks
- 1.33 lines changed: 6, context: html, text, full: html, text
Switched all chainFelCat3 and netFelCat3 tracks to be composite chainNetFelCat3 tracks.
- src/hg/makeDb/trackDb/drosophila/all_est.html
- 1.6 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/drosophila/all_mrna.html
- 1.4 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/drosophila/dp1/xenoDrosEst.html
- 1.7 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/drosophila/dp1/xenoDrosMrna.html
- 1.6 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/drosophila/est.html
- 1.5 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/drosophila/intronEst.html
- 1.8 lines changed: 1, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/drosophila/mrna.html
- 1.5 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/drosophila/xenoMrna.html
- 1.5 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/fugu/intronEst.html
- 1.6 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/fugu/trackDb.ra
- 1.71 lines changed: 26, context: html, text, full: html, text
moved all galGal3 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/fugu/xenoMrna.html
- 1.6 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/guineaPig/trackDb.chainNet.ra
- 1.6 lines changed: 3, context: html, text, full: html, text
adding Panda and Pig chainNet composite tracks
- src/hg/makeDb/trackDb/horse/trackDb.ra
- 1.23 lines changed: 6, context: html, text, full: html, text
moved all galGal3 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/human/gwasCatalog.html
- 1.1 lines changed: 0, context: html, text, full: html, text
Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies).
- src/hg/makeDb/trackDb/human/hg16/hg17Kg.html
- 1.5 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/human/hg16/trackDb.ra
- 1.583 lines changed: 18, context: html, text, full: html, text
moved all galGal22 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/human/hg17/knownGene.html
- 1.9 lines changed: 8, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/human/hg17/trackDb.chainNet.ra
- 1.12 lines changed: 3, context: html, text, full: html, text
Changing opossum net and chain tracks to composites. The following assemblies are currently live on the RR: calJac1 canFam2 cavPor3 danRer4 danRer5 galGal2 galGal3 hg17 hg18 hg19 mm8 mm9 ornAna1 panTro2 ponAbe2 rheMac2 rn4 xenTro2.
- 1.11 lines changed: 1, context: html, text, full: html, text
moved all panTro1 chains and nets to composite and dropped individual tracks. only hg17 and mm7 on RR
- src/hg/makeDb/trackDb/human/hg17/trackDb.ra
- 1.440 lines changed: 50, context: html, text, full: html, text
Changing opossum net and chain tracks to composites. The following assemblies are currently live on the RR: calJac1 canFam2 cavPor3 danRer4 danRer5 galGal2 galGal3 hg17 hg18 hg19 mm8 mm9 ornAna1 panTro2 ponAbe2 rheMac2 rn4 xenTro2.
- 1.439 lines changed: 16, context: html, text, full: html, text
moved all galGal22 chains and nets to composite and dropped individual tracks
- 1.438 lines changed: 24, context: html, text, full: html, text
moved all rheMac2 chains and nets to composite and dropped individual tracks
- 1.437 lines changed: 6, context: html, text, full: html, text
moved all panTro1 chains and nets to composite and dropped individual tracks. only hg17 and mm7 on RR
- src/hg/makeDb/trackDb/human/hg18/knownGene.html
- 1.31 lines changed: 1, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/human/hg18/knownGeneOld2.html
- 1.4 lines changed: 1, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/human/hg18/pgSnp.html
- 1.12 lines changed: 2, context: html, text, full: html, text
Oops, forgot to use < instead of bare < .
- 1.11 lines changed: 3, context: html, text, full: html, text
Corrections: Venter and Illumina's Yoruban variants are not just single-base. Thanks Mark!
- src/hg/makeDb/trackDb/human/hg18/trackDb.ra
- 1.457 lines changed: 29, context: html, text, full: html, text
Changing opossum net and chain tracks to composites. The following assemblies are currently live on the RR: calJac1 canFam2 cavPor3 danRer4 danRer5 galGal2 galGal3 hg17 hg18 hg19 mm8 mm9 ornAna1 panTro2 ponAbe2 rheMac2 rn4 xenTro2.
- 1.456 lines changed: 28, context: html, text, full: html, text
moved all rheMac2 chains and nets to composite and dropped individual tracks
- 1.455 lines changed: 28, context: html, text, full: html, text
moved all panTro2 chains and nets to composite and dropped individual tracks
- 1.454 lines changed: 12, context: html, text, full: html, text
moved all panTro1 chains and nets to composite and dropped individual tracks. only hg17 and mm7 on RR
- src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
- 1.835 lines changed: 25, context: html, text, full: html, text
Fixed SREBP1A to SREBP1 fro Yale and added missing protocol tper for 8 HAIB subtracks
- 1.834 lines changed: 17, context: html, text, full: html, text
Fix TFIIIC to TFIIIC-110 for Yale
- 1.833 lines changed: 2, context: html, text, full: html, text
oops one more place
- 1.832 lines changed: 9, context: html, text, full: html, text
fix up ENCODE Riken to change Hepg2 LongnonPolyA to hepg2 total
- 1.831 lines changed: 104, context: html, text, full: html, text
Cleaned up some metadata for HAIB
- 1.830 lines changed: 13, context: html, text, full: html, text
fix up the ENCODE BU orchid tracks
- 1.829 lines changed: 17, context: html, text, full: html, text
HAIB needed Oct-2 changed to POU2F2
- 1.828 lines changed: 263, context: html, text, full: html, text
Removed release alphas to stage UW chip seq track.
- 1.827 lines changed: 92, context: html, text, full: html, text
first cut at Orchid/Chai tracks
- 1.826 lines changed: 2, context: html, text, full: html, text
Standardize lab name for UT-Austin
- 1.825 lines changed: 8, context: html, text, full: html, text
fix up some CSHL small RNA short labels
- 1.824 lines changed: 136, context: html, text, full: html, text
shorten up Caltech labels
- 1.823 lines changed: 4, context: html, text, full: html, text
Fixed a couple of HU TFSB subGroup mistakes
- 1.822 lines changed: 10, context: html, text, full: html, text
Minor revisions to some long labels
- 1.821 lines changed: 40, context: html, text, full: html, text
Added submission # 1060
- 1.820 lines changed: 7, context: html, text, full: html, text
Fixed some shortLabels for Duke
- 1.819 lines changed: 57, context: html, text, full: html, text
Added one more cell type for Hudson Alpha chipseq
- 1.818 lines changed: 41, context: html, text, full: html, text
added UW DGF tracks
- 1.817 lines changed: 14, context: html, text, full: html, text
fix short labels and add some useScores for HA RNA-seq
- 1.816 lines changed: 9, context: html, text, full: html, text
Added one last forgotten submission for Yale Jan 2010 freeze
- 1.815 lines changed: 31, context: html, text, full: html, text
Fixed some RepK562 to Rep1K562 errors
- 1.814 lines changed: 327, context: html, text, full: html, text
added UW DGF tracks
- 1.813 lines changed: 37, context: html, text, full: html, text
HudsonAlpha MethylSeq Gm12892 Gm12891
- 1.812 lines changed: 50, context: html, text, full: html, text
wgEncodeCaltechRnaSeqPlusRawSignalRep1H1hescCellPapBb2R1x75d
- 1.811 lines changed: 2, context: html, text, full: html, text
Oops, accidentally swapped the wrong composites' dimensions
- 1.810 lines changed: 329, context: html, text, full: html, text
Added final 10 UW DnaseI submissions for Jan 2010 freeze
- 1.809 lines changed: 30, context: html, text, full: html, text
wgEncodeCaltechRnaSeqRawSignalRep2H1hescCellPapBb2R2x75
- 1.808 lines changed: 50, context: html, text, full: html, text
wgEncodeCaltechRnaSeqSplicesRep2Helas3CellPapBlat34R1x75d
- 1.807 lines changed: 50, context: html, text, full: html, text
wgEncodeCaltechRnaSeqSplicesRep1HuvecCellPapBlat34R1x75d
- 1.806 lines changed: 50, context: html, text, full: html, text
wgEncodeCaltechRnaSeqSplicesRep1Helas3CellPapBlat34R1x75d
- 1.805 lines changed: 30, context: html, text, full: html, text
wgEncodeCaltechRnaSeqPairedRep1H1hescCellPapErng32aR2x75
- 1.804 lines changed: 30, context: html, text, full: html, text
wgEncodeCaltechRnaSeqRawSignalRep1HuvecCellPapBb2R2x75
- 1.803 lines changed: 30, context: html, text, full: html, text
wgEncodeCaltechRnaSeqRawSignalRep2HuvecCellPapBb2R2x75
- 1.802 lines changed: 30, context: html, text, full: html, text
wgEncodeCaltechRnaSeqSplicesRep1NhekCellPapBb2R2x75
- 1.801 lines changed: 30, context: html, text, full: html, text
wgEncodeCaltechRnaSeqPairedRep2Helas3CellPapErng32aR2x75
- 1.800 lines changed: 31, context: html, text, full: html, text
altechRnaSeqSplicesRep1Helas3CellPapBb2R2x75
- 1.799 lines changed: 467, context: html, text, full: html, text
Added 17 more submissions for UW DNaseI Jan 2010 freeze
- 1.798 lines changed: 50, context: html, text, full: html, text
wgEncodeCaltechRnaSeqMinusRawSignalRep1Hepg2CellPapBb2R1x75d
- 1.797 lines changed: 50, context: html, text, full: html, text
wgEncodeCaltechRnaSeqPlusRawSignalRep2Hepg2CellPapBb2R1x75d
- 1.796 lines changed: 332, context: html, text, full: html, text
Added 13 submissions for UW DNaseI Jan 2010 freeze
- 1.795 lines changed: 51, context: html, text, full: html, text
wgEncodeCaltechRnaSeqMinusRawSignalRep2HuvecCellPapBb2R1x75d
- 1.794 lines changed: 30, context: html, text, full: html, text
wgEncodeCaltechRnaSeqRawSignalRep2Gm12878CellPapBb2R2x75Il400
- 1.793 lines changed: 31, context: html, text, full: html, text
wgEncodeCaltechRnaSeqRawSignalRep1H1hescCellPapBb2R2x75Il400
- 1.792 lines changed: 30, context: html, text, full: html, text
wgEncodeCaltechRnaSeqRawSignalRep4H1hescCellPapBb2R2x75
- 1.791 lines changed: 30, context: html, text, full: html, text
Caltech RNA-seq HepG2 rep1 single reads
- 1.790 lines changed: 30, context: html, text, full: html, text
wgEncodeCaltechRnaSeqRawSignalRep2Hepg2CellPapBb2R1x32
- 1.789 lines changed: 361, context: html, text, full: html, text
added UW ChIP tracks
- 1.788 lines changed: 41, context: html, text, full: html, text
wgEncodeHudsonalphaRnaSeqRPKMRep2JurkatCellPapBow10R1x25
- 1.787 lines changed: 81, context: html, text, full: html, text
Added 4 more submissions for Yale Harvard(Struhl) for Jan 2010 freeze. Could this be it for Yale
- 1.786 lines changed: 141, context: html, text, full: html, text
Added 7 submissions for Yale Harvard(Struhl) for Jan 2010 freeze
- 1.785 lines changed: 81, context: html, text, full: html, text
Four more submissions for Yale Snyder Jan 2010 freeze
- 1.784 lines changed: 60, context: html, text, full: html, text
Three more Yale, this time IFNs for Jan 2010
- 1.783 lines changed: 61, context: html, text, full: html, text
Three more Yale IgG submissions for Jan 2010
- 1.782 lines changed: 204, context: html, text, full: html, text
Added Yale forskolin and insulin submissions for Jan 2010 freeze
- 1.781 lines changed: 73, context: html, text, full: html, text
Added Yale Stanford(Snyder) Rabbit_IgG submissions for Jan 2010 freeze
- 1.780 lines changed: 30, context: html, text, full: html, text
CSHL short (short in K562 cell) alignments and signals
- 1.779 lines changed: 572, context: html, text, full: html, text
Added Yale Stanford(Snyder)s musIgG submissions for Jam 2010 freeze
- 1.778 lines changed: 30, context: html, text, full: html, text
Riken Cage HepG2 alignments
- 1.777 lines changed: 61, context: html, text, full: html, text
RIKEN CAGE HepG2
- 1.776 lines changed: 30, context: html, text, full: html, text
wgEncodeCshlShortRnaSeqAlignmentsGm12878CellShort
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.html
- 1.20 lines changed: 7, context: html, text, full: html, text
Altered 'notes' to clarify 'protocol'
- src/hg/makeDb/trackDb/human/hg18/wgEncodeUwChIPSeq.html
- 1.5 lines changed: 5, context: html, text, full: html, text
Minor correction to 'display conventions' text
- src/hg/makeDb/trackDb/human/hg19/knownGene.html
- 1.4 lines changed: 1, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/human/hg19/pgSnp.html
- 1.1 lines changed: 0, context: html, text, full: html, text
Belinda's liftOver'd personal genome variants.
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- 1.85 lines changed: 18, context: html, text, full: html, text
Got a little overzealous on last commit. Changing this back so felCat3 stays in the placental group.
- 1.84 lines changed: 18, context: html, text, full: html, text
Switched all chainFelCat3 and netFelCat3 tracks to be composite chainNetFelCat3 tracks.
- src/hg/makeDb/trackDb/human/trackDb.ra
- 1.500 lines changed: 40, context: html, text, full: html, text
Changing opossum net and chain tracks to composites. The following assemblies are currently live on the RR: calJac1 canFam2 cavPor3 danRer4 danRer5 galGal2 galGal3 hg17 hg18 hg19 mm8 mm9 ornAna1 panTro2 ponAbe2 rheMac2 rn4 xenTro2.
- 1.499 lines changed: 13, context: html, text, full: html, text
Switching equCab1 and equCab2 chains and nets to composites. EquCab1 is currently on RR for hg18, mm8, panTro2 and rn4. EquCab1 is on RR for canFam2, galGal3, hg19, mm9, monDom5, ornaAna1.
- 1.498 lines changed: 4, context: html, text, full: html, text
Adding snpTable and snpVersion (and url, urlLabel) to gwasCatalog.
- 1.497 lines changed: 4, context: html, text, full: html, text
moved all calJac1 chains and nets to composite and dropped individual tracks
- 1.496 lines changed: 1, context: html, text, full: html, text
Bumped up gwasCatalog's searchPriority, Jim's request.
- 1.495 lines changed: 1, context: html, text, full: html, text
Change gwasCatalog color from blue to green (neighboring tracks are blue).
- 1.494 lines changed: 17, context: html, text, full: html, text
Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies).
- src/hg/makeDb/trackDb/intronEst.html
- 1.27 lines changed: 1, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/knownGene.html
- 1.18 lines changed: 1, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/lizard/trackDb.ra
- 1.9 lines changed: 6, context: html, text, full: html, text
moved all galGal3 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/lowelab/BlastP_ArchaeaOther.html
- 1.1 lines changed: 0, context: html, text, full: html, text
add blastp track description
- src/hg/makeDb/trackDb/lowelab/BlastP_Viruses.html
- 1.1 lines changed: 0, context: html, text, full: html, text
add blastp track description
- src/hg/makeDb/trackDb/lowelab/franPhil_ATCC25017/trackDb.ra
- src/hg/makeDb/trackDb/lowelab/franTula_FSC_198/trackDb.ra
- src/hg/makeDb/trackDb/lowelab/franTula_HOLARCTICA_1/trackDb.ra
- src/hg/makeDb/trackDb/lowelab/franTula_HOLARCTICA_OSU18/trackDb.ra
- src/hg/makeDb/trackDb/marmoset/trackDb.ra
- 1.11 lines changed: 6, context: html, text, full: html, text
moved all rheMac2 chains and nets to composite and dropped individual tracks
- 1.10 lines changed: 4, context: html, text, full: html, text
moved all panTro2 chains and nets to composite and dropped individual tracks
- 1.9 lines changed: 5, context: html, text, full: html, text
moved all ponAbe2 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/mouse/mm6/knownGene.html
- 1.15 lines changed: 10, context: html, text, full: html, text
Edited UCSC Genes ref to current ref standards
- 1.14 lines changed: 8, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/mouse/mm7/knownGene.html
- 1.11 lines changed: 10, context: html, text, full: html, text
Edited UCSC Genes ref to current ref standards
- 1.10 lines changed: 1, context: html, text, full: html, text
moved all panTro2 chains and nets to composite and dropped individual tracks
- 1.9 lines changed: 8, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/mouse/mm7/trackDb.chainNet.ra
- 1.9 lines changed: 1, context: html, text, full: html, text
moved all panTro1 chains and nets to composite and dropped individual tracks. only hg17 and mm7 on RR
- src/hg/makeDb/trackDb/mouse/mm8/knownGene.html
- 1.8 lines changed: 10, context: html, text, full: html, text
Edited UCSC Genes ref to current ref standards
- 1.7 lines changed: 1, context: html, text, full: html, text
moved all panTro2 chains and nets to composite and dropped individual tracks
- 1.6 lines changed: 8, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/mouse/mm9/knownGene.html
- 1.2 lines changed: 1, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.chainNet.ra
- 1.4 lines changed: 3, context: html, text, full: html, text
Switching equCab1 and equCab2 chains and nets to composites. EquCab1 is currently on RR for hg18, mm8, panTro2 and rn4. EquCab1 is on RR for canFam2, galGal3, hg19, mm9, monDom5, ornaAna1.
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
- 1.76 lines changed: 8, context: html, text, full: html, text
Changing opossum net and chain tracks to composites. The following assemblies are currently live on the RR: calJac1 canFam2 cavPor3 danRer4 danRer5 galGal2 galGal3 hg17 hg18 hg19 mm8 mm9 ornAna1 panTro2 ponAbe2 rheMac2 rn4 xenTro2.
- src/hg/makeDb/trackDb/mouse/mm9/transcriptome.html
- 1.2 lines changed: 1, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
- 1.28 lines changed: 1, context: html, text, full: html, text
moved all panTro1 chains and nets to composite and dropped individual tracks. only hg17 and mm7 on RR
- 1.27 lines changed: 6, context: html, text, full: html, text
adding Panda and Pig chainNet composite tracks
- src/hg/makeDb/trackDb/mouse/trackDb.ra
- 1.190 lines changed: 28, context: html, text, full: html, text
Changing opossum net and chain tracks to composites. The following assemblies are currently live on the RR: calJac1 canFam2 cavPor3 danRer4 danRer5 galGal2 galGal3 hg17 hg18 hg19 mm8 mm9 ornAna1 panTro2 ponAbe2 rheMac2 rn4 xenTro2.
- 1.189 lines changed: 7, context: html, text, full: html, text
moved all rheMac2 chains and nets to composite and dropped individual tracks
- 1.188 lines changed: 28, context: html, text, full: html, text
moved all panTro2 chains and nets to composite and dropped individual tracks
- 1.187 lines changed: 8, context: html, text, full: html, text
moved all panTro1 chains and nets to composite and dropped individual tracks. only hg17 and mm7 on RR
- 1.186 lines changed: 13, context: html, text, full: html, text
moved all ponAbe2 chains and nets to composite and dropped individual tracks
- 1.185 lines changed: 7, context: html, text, full: html, text
Switching equCab1 and equCab2 chains and nets to composites. EquCab1 is currently on RR for hg18, mm8, panTro2 and rn4. EquCab1 is on RR for canFam2, galGal3, hg19, mm9, monDom5, ornaAna1.
- 1.184 lines changed: 7, context: html, text, full: html, text
moved all calJac1 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/opossum/monDom4/trackDb.chainNet.ra
- 1.9 lines changed: 1, context: html, text, full: html, text
moved all galGal22 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/opossum/monDom5/trackDb.chainNet.ra
- 1.5 lines changed: 8, context: html, text, full: html, text
moved all galGal3 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra
- 1.29 lines changed: 17, context: html, text, full: html, text
moved all galGal3 chains and nets to composite and dropped individual tracks
- 1.28 lines changed: 10, context: html, text, full: html, text
moved all rheMac2 chains and nets to composite and dropped individual tracks
- 1.27 lines changed: 10, context: html, text, full: html, text
moved all panTro2 chains and nets to composite and dropped individual tracks
- 1.26 lines changed: 10, context: html, text, full: html, text
moved all ponAbe2 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/opossum/trackDb.chainNet.ra
- 1.16 lines changed: 5, context: html, text, full: html, text
adding Panda and Pig chainNet composite tracks
- src/hg/makeDb/trackDb/opossum/trackDb.ra
- 1.43 lines changed: 17, context: html, text, full: html, text
moved all galGal22 chains and nets to composite and dropped individual tracks
- 1.42 lines changed: 28, context: html, text, full: html, text
moved all panTro2 chains and nets to composite and dropped individual tracks
- 1.41 lines changed: 7, context: html, text, full: html, text
moved all calJac1 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/orangutan/trackDb.ra
- 1.11 lines changed: 8, context: html, text, full: html, text
Changing opossum net and chain tracks to composites. The following assemblies are currently live on the RR: calJac1 canFam2 cavPor3 danRer4 danRer5 galGal2 galGal3 hg17 hg18 hg19 mm8 mm9 ornAna1 panTro2 ponAbe2 rheMac2 rn4 xenTro2.
- 1.10 lines changed: 6, context: html, text, full: html, text
moved all panTro2 chains and nets to composite and dropped individual tracks
- 1.9 lines changed: 3, context: html, text, full: html, text
moved all calJac1 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/panda/ailMel1/description.html
- 1.3 lines changed: 1, context: html, text, full: html, text
some border space around the photo
- 1.2 lines changed: 24, context: html, text, full: html, text
updated description with appropriate links
- src/hg/makeDb/trackDb/panda/trackDb.chainNet.ra
- 1.1 lines changed: 0, context: html, text, full: html, text
adding priorities for dog, rat, mouse, human chain nets
- src/hg/makeDb/trackDb/panda/trackDb.ra
- 1.1 lines changed: 0, context: html, text, full: html, text
adding priorities for dog, rat, mouse, human chain nets
- src/hg/makeDb/trackDb/pig/susScr1/description.html
- 1.3 lines changed: 1, context: html, text, full: html, text
some border space around the photo
- 1.2 lines changed: 23, context: html, text, full: html, text
updated description with appropriate links
- src/hg/makeDb/trackDb/pig/trackDb.chainNet.ra
- 1.1 lines changed: 0, context: html, text, full: html, text
adding chain net priorities for mouse human and opossum
- src/hg/makeDb/trackDb/pig/trackDb.ra
- 1.1 lines changed: 0, context: html, text, full: html, text
adding chain net priorities for mouse human and opossum
- src/hg/makeDb/trackDb/platypus/ornAna1/trackDb.ra
- 1.20 lines changed: 10, context: html, text, full: html, text
Changing opossum net and chain tracks to composites. The following assemblies are currently live on the RR: calJac1 canFam2 cavPor3 danRer4 danRer5 galGal2 galGal3 hg17 hg18 hg19 mm8 mm9 ornAna1 panTro2 ponAbe2 rheMac2 rn4 xenTro2.
- 1.19 lines changed: 9, context: html, text, full: html, text
moved all ponAbe2 chains and nets to composite and dropped individual tracks
- 1.18 lines changed: 8, context: html, text, full: html, text
moved all calJac1 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/platypus/trackDb.ra
- 1.14 lines changed: 27, context: html, text, full: html, text
Switching equCab1 and equCab2 chains and nets to composites. EquCab1 is currently on RR for hg18, mm8, panTro2 and rn4. EquCab1 is on RR for canFam2, galGal3, hg19, mm9, monDom5, ornaAna1.
- 1.13 lines changed: 3, context: html, text, full: html, text
moved all calJac1 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/rabbit/oryCun2/description.html
- 1.3 lines changed: 22, context: html, text, full: html, text
fixup sample searches and finalize assembly description
- 1.2 lines changed: 17, context: html, text, full: html, text
fixing up Broad links
- src/hg/makeDb/trackDb/rabbit/oryCun2/trackDb.ra
- 1.2 lines changed: 10, context: html, text, full: html, text
adjusting some track default visibilities
- src/hg/makeDb/trackDb/rat/rn3/knownGene.html
- 1.7 lines changed: 10, context: html, text, full: html, text
Edited UCSC Genes ref to current ref standards
- 1.6 lines changed: 8, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/rat/rn4/knownGene.html
- 1.7 lines changed: 10, context: html, text, full: html, text
Edited UCSC Genes ref to current ref standards
- 1.6 lines changed: 8, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
- 1.49 lines changed: 28, context: html, text, full: html, text
moved all panTro2 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/rat/trackDb.chainNet.ra
- 1.16 lines changed: 8, context: html, text, full: html, text
adding Panda and Pig chainNet composite tracks
- src/hg/makeDb/trackDb/rat/trackDb.ra
- 1.69 lines changed: 14, context: html, text, full: html, text
moved all galGal3 chains and nets to composite and dropped individual tracks
- 1.68 lines changed: 14, context: html, text, full: html, text
moved all rheMac2 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
- 1.52 lines changed: 28, context: html, text, full: html, text
moved all panTro2 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/rhesus/trackDb.ra
- 1.20 lines changed: 9, context: html, text, full: html, text
moved all ponAbe2 chains and nets to composite and dropped individual tracks
- 1.19 lines changed: 7, context: html, text, full: html, text
moved all calJac1 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/rnaCluster.html
- 1.13 lines changed: 1, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/sacCer/mrna.html
- 1.3 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/sars/sc1/all_mrna.html
- 1.5 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/sars/sc1/xenoBlastzMrna.html
- 1.7 lines changed: 6, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/sars/sc1/xenoMrna.html
- 1.7 lines changed: 6, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/sibGene.html
- 1.3 lines changed: 1, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/squirt/all_est.html
- 1.5 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/squirt/all_mrna.html
- 1.3 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/squirt/intronEst.html
- 1.6 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/squirt/xenoMrna.html
- 1.4 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/stickleback/trackDb.ra
- 1.25 lines changed: 27, context: html, text, full: html, text
moved all galGal3 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/tRNAs.html
- 1.2 lines changed: 13, context: html, text, full: html, text
Slightly updated description to include info on what tRNA score means.
- src/hg/makeDb/trackDb/tagTypes.tab
- 1.8 lines changed: 2, context: html, text, full: html, text
Adding snpTable and snpVersion (and url, urlLabel) to gwasCatalog.
- 1.7 lines changed: 1, context: html, text, full: html, text
add subbGroup8
- src/hg/makeDb/trackDb/tetraodon/est.html
- 1.7 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/tetraodon/intronEst.html
- 1.9 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/tetraodon/mrna.html
- 1.6 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/tetraodon/xenoMrna.html
- 1.7 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/trackDb.chainNet.ra
- 1.50 lines changed: 96, context: html, text, full: html, text
Changed all entries to have a color of black and an altColor of dark brown. The old altColor of tan was showing up on chains within composites and was nearly impossible to see.
- 1.49 lines changed: 4, context: html, text, full: html, text
moved all galGal3 chains and nets to composite and dropped individual tracks
- 1.48 lines changed: 10, context: html, text, full: html, text
Removing release alphas on chainNetMonDom tracks. Also changing color to black, to make the chain longLabels show up against white.
- 1.47 lines changed: 4, context: html, text, full: html, text
moved all galGal22 chains and nets to composite and dropped individual tracks
- 1.46 lines changed: 6, context: html, text, full: html, text
moved all rheMac2 chains and nets to composite and dropped individual tracks
- 1.45 lines changed: 3, context: html, text, full: html, text
moved all panTro2 chains and nets to composite and dropped individual tracks
- 1.44 lines changed: 6, context: html, text, full: html, text
moved all panTro1 chains and nets to composite and dropped individual tracks. only hg17 and mm7 on RR
- 1.43 lines changed: 3, context: html, text, full: html, text
moved all ponAbe2 chains and nets to composite and dropped individual tracks
- 1.42 lines changed: 4, context: html, text, full: html, text
Switching equCab1 and equCab2 chains and nets to composites. EquCab1 is currently on RR for hg18, mm8, panTro2 and rn4. EquCab1 is on RR for canFam2, galGal3, hg19, mm9, monDom5, ornaAna1.
- 1.41 lines changed: 98, context: html, text, full: html, text
adding Panda and Pig chainNet composite tracks
- 1.40 lines changed: 65, context: html, text, full: html, text
Set all of the net tracks within composite chainNet tracks to full.
- 1.39 lines changed: 3, context: html, text, full: html, text
moved all calJac1 chains and nets to composite and dropped individual tracks
- 1.38 lines changed: 3, context: html, text, full: html, text
Switched all chainFelCat3 and netFelCat3 tracks to be composite chainNetFelCat3 tracks.
- src/hg/makeDb/trackDb/trackDb.ra
- 1.594 lines changed: 26, context: html, text, full: html, text
moved all galGal3 chains and nets to composite and dropped individual tracks
- 1.593 lines changed: 51, context: html, text, full: html, text
Changing opossum net and chain tracks to composites. The following assemblies are currently live on the RR: calJac1 canFam2 cavPor3 danRer4 danRer5 galGal2 galGal3 hg17 hg18 hg19 mm8 mm9 ornAna1 panTro2 ponAbe2 rheMac2 rn4 xenTro2.
- 1.592 lines changed: 27, context: html, text, full: html, text
moved all galGal22 chains and nets to composite and dropped individual tracks
- 1.591 lines changed: 26, context: html, text, full: html, text
moved all rheMac2 chains and nets to composite and dropped individual tracks
- 1.590 lines changed: 26, context: html, text, full: html, text
moved all panTro2 chains and nets to composite and dropped individual tracks
- 1.589 lines changed: 25, context: html, text, full: html, text
moved all panTro1 chains and nets to composite and dropped individual tracks. only hg17 and mm7 on RR
- 1.588 lines changed: 22, context: html, text, full: html, text
Removing blocks for monDom2 chains and nets. These do not exist anywhere.
- 1.587 lines changed: 26, context: html, text, full: html, text
moved all ponAbe2 chains and nets to composite and dropped individual tracks
- 1.586 lines changed: 22, context: html, text, full: html, text
dropped track blocks for chain and netPonAbe1, as no assembly has these tracks
- 1.585 lines changed: 28, context: html, text, full: html, text
Switching equCab1 and equCab2 chains and nets to composites. EquCab1 is currently on RR for hg18, mm8, panTro2 and rn4. EquCab1 is on RR for canFam2, galGal3, hg19, mm9, monDom5, ornaAna1.
- 1.584 lines changed: 26, context: html, text, full: html, text
moved all calJac1 chains and nets to composite and dropped individual tracks
- 1.583 lines changed: 30, context: html, text, full: html, text
Switched all chainFelCat3 and netFelCat3 tracks to be composite chainNetFelCat3 tracks.
- src/hg/makeDb/trackDb/worm/ce4/transcriptome.html
- 1.2 lines changed: 1, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/worm/ce6/algBinding.html
- 1.3 lines changed: 2, context: html, text, full: html, text
italicizing scientific name
- src/hg/makeDb/trackDb/worm/intronEst.html
- 1.7 lines changed: 1, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/worm/xenoMrna.html
- 1.5 lines changed: 1, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/xenTro/all_est.html
- 1.5 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/xenTro/all_mrna.html
- 1.3 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/xenTro/intronEst.html
- 1.6 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/xenTro/xenTro1/trackDb.ra
- 1.42 lines changed: 17, context: html, text, full: html, text
moved all galGal22 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/xenTro/xenTro2/trackDb.ra
- 1.22 lines changed: 27, context: html, text, full: html, text
Changing opossum net and chain tracks to composites. The following assemblies are currently live on the RR: calJac1 canFam2 cavPor3 danRer4 danRer5 galGal2 galGal3 hg17 hg18 hg19 mm8 mm9 ornAna1 panTro2 ponAbe2 rheMac2 rn4 xenTro2.
- src/hg/makeDb/trackDb/xenoBestMrna.html
- 1.12 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/xenoEst.html
- 1.14 lines changed: 7, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/xenoMrna.html
- 1.27 lines changed: 1, context: html, text, full: html, text
Finally decided to take the plunge and edit the citations for the genbank
references.
- src/hg/makeDb/trackDb/zebraFinch/trackDb.ra
- 1.9 lines changed: 22, context: html, text, full: html, text
moved all galGal3 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/zebrafish/danRer3/trackDb.ra
- 1.57 lines changed: 7, context: html, text, full: html, text
Removed blocks for chains and nets to monDom2.
- src/hg/makeDb/trackDb/zebrafish/danRer4/trackDb.ra
- 1.41 lines changed: 28, context: html, text, full: html, text
moved all panTro2 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/zebrafish/trackDb.ra
- 1.64 lines changed: 41, context: html, text, full: html, text
Changing opossum net and chain tracks to composites. The following assemblies are currently live on the RR: calJac1 canFam2 cavPor3 danRer4 danRer5 galGal2 galGal3 hg17 hg18 hg19 mm8 mm9 ornAna1 panTro2 ponAbe2 rheMac2 rn4 xenTro2.
- src/hg/qaPushQ/qaPushQ.c
- 1.118 lines changed: 1, context: html, text, full: html, text
increased html buffer size for handling huge ENCODE lists
- 1.117 lines changed: 1, context: html, text, full: html, text
increasing the sizes of lists
- src/hg/tcga/pBamBam/makefile
- 1.4 lines changed: 7, context: html, text, full: html, text
added mutation specific code for testing
- src/hg/tcga/pBamBam/pBamBamMuts.c
- 1.1 lines changed: 0, context: html, text, full: html, text
added mutation specific code for testing
- src/hg/utils/phyloTrees/48way.dissect.txt
- 1.1 lines changed: 0, context: html, text, full: html, text
update to a 48-way tree while maintaining same priorities for previous 46-way
- src/hg/utils/phyloTrees/48way.nh
- 1.1 lines changed: 0, context: html, text, full: html, text
update to a 48-way tree while maintaining same priorities for previous 46-way
- src/hg/utils/phyloTrees/chainNet.pl
- 1.4 lines changed: 15, context: html, text, full: html, text
update to a 48-way tree while maintaining same priorities for previous 46-way
- src/hg/utils/refSeqGet/refSeqGet.c
- 1.3 lines changed: 2, context: html, text, full: html, text
fixed ussage message
- src/hg/utils/refreshNamedSessionCustomTracks/refreshSessionCtFilesInner.csh
- 1.4 lines changed: 1, context: html, text, full: html, text
Adding -atime=123 option to refreshNamedSessionCustomTracks, so we will no longer refresh files in sessions that have not been accessed in >4 months.
- src/utils/qa/checkMachineName.csh
- 1.6 lines changed: 1, context: html, text, full: html, text
fixed getAssemblies.csh to work with RR machines and several other programs that it depends on. it broke when we went to a single mysql machine and genbank dumps only grab from hgnfs1
- src/utils/qa/countPerChrom.csh
- 1.15 lines changed: 39, context: html, text, full: html, text
added support for second set of data in histogram
- 1.14 lines changed: 46, context: html, text, full: html, text
made graph.csh to draw a bar graph from a two-column file and added option for countPerChrom.csh to use it
- src/utils/qa/getAssemblies.csh
- 1.23 lines changed: 38, context: html, text, full: html, text
fixed getAssemblies.csh to work with RR machines and several other programs that it depends on. it broke when we went to a single mysql machine and genbank dumps only grab from hgnfs1
- src/utils/qa/getRRdatabases.csh
- 1.12 lines changed: 11, context: html, text, full: html, text
fixed getAssemblies.csh to work with RR machines and several other programs that it depends on. it broke when we went to a single mysql machine and genbank dumps only grab from hgnfs1
- src/utils/qa/getRRtables.csh
- 1.6 lines changed: 10, context: html, text, full: html, text
fixed getAssemblies.csh to work with RR machines and several other programs that it depends on. it broke when we went to a single mysql machine and genbank dumps only grab from hgnfs1
- src/utils/qa/graph.csh
- 1.3 lines changed: 17, context: html, text, full: html, text
added formatting for variable first column width
- 1.2 lines changed: 5, context: html, text, full: html, text
forgot to implement configurable bar length after adding option in usage statement
- 1.1 lines changed: 22, context: html, text, full: html, text
made graph.csh to draw a bar graph from a two-column file and added option for countPerChrom.csh to use it
- src/utils/qa/makefile
- 1.117 lines changed: 1, context: html, text, full: html, text
made graph.csh to draw a bar graph from a two-column file and added option for countPerChrom.csh to use it
- src/utils/qa/qaEncodeTracks.csh
- 1.5 lines changed: 60, context: html, text, full: html, text
Edited so that, in general, it only prints output if there is a problem. Removed
lots of extra lines. Added a couple of defined values. General clean-up.
- 1.4 lines changed: 10, context: html, text, full: html, text
commented out featureBits run
- src/utils/qa/syncAday.csh
- 1.10 lines changed: 4, context: html, text, full: html, text
removed checking for multiple RR machines since we've gone to single mysql database
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 12282
- files changed: 216