All File Changes
v258_preview to v258_preview2 (2011-09-27 to 2011-10-04) v258
- python/lib/ucscgenomics/cv.py
- python/programs/cvValidate/cvValidate
- src/hg/encode/DAFs/3.0/hg19/wgEncodeBuOrchid.daf
- lines changed 33, context: html, text, full: html, text
Adding more DAFs to the 3.0 directory
- src/hg/encode/DAFs/3.0/hg19/wgEncodeHaibTfbs.daf
- lines changed 10, context: html, text, full: html, text
Adding more DAFs to the 3.0 directory
- src/hg/encode/DAFs/3.0/hg19/wgEncodeOpenChromSynth.daf
- lines changed 28, context: html, text, full: html, text
Adding more DAFs to the 3.0 directory
- src/hg/encode/encodeAnnounce/encodeAnnounce.pl
- lines changed 1, context: html, text, full: html, text
Minor cleanup (remove double slashes where single can do)
- src/hg/encode/encodeDownloadReadme/encodeDownloadReadme.pl
- lines changed 0, context: html, text, full: html, text
cleaned up some whitespace stuff
- src/hg/hgCustom/hgCustom.c
- lines changed 4, context: html, text, full: html, text
Feature #986 (VCF+tabix): mention VCF in hgCustom's list of supported formats.
- src/hg/hgTracks/hgTracks.c
- lines changed 32, context: html, text, full: html, text
moved PS/PDF and Sessions links in topbar to the left of NCBI and Ensembl links so they are onscreen in narrow windows
- src/hg/hgTracks/makefile
- lines changed 1, context: html, text, full: html, text
cleanup based on angie's code review comments
- src/hg/hgTracks/makefile.hgRenderTracks
- lines changed 2, context: html, text, full: html, text
cleanup based on angie's code review comments
- src/hg/hgc/hgc.c
- lines changed 7, context: html, text, full: html, text
Updated logic of omimGene2 for RefSeq to deal with if previous RefSeq no longer available.
- lines changed 68, context: html, text, full: html, text
put back logic to handle geneReviews track using the geneReviews table in the database
- lines changed 11, context: html, text, full: html, text
Do not do geneReviews for non-human species
- src/hg/hgc/hgc.h
- lines changed 6, context: html, text, full: html, text
put back logic to handle geneReviews track using the geneReviews table in the database
- src/hg/htdocs/ENCODE/downloads.html
- lines changed 10, context: html, text, full: html, text
adding UNC/BSE ProtGeno and its supertrack, redmine 141
- src/hg/htdocs/ENCODE/index.html
- lines changed 36, context: html, text, full: html, text
Add Summer human data releases. TODO: retire older ones to news archives. TODO: Add late summer Mouse
- lines changed 6, context: html, text, full: html, text
removing extraneous '/' from the urls
- src/hg/htdocs/FAQ/FAQformat.html
- lines changed 10, context: html, text, full: html, text
Added lines to the GFF and GenePred sections referring users to the wiki article for converting from GenePred to GTF
- lines changed 52, context: html, text, full: html, text
Feature #986 (VCF+tabix): Added VCF to FAQformat.
- src/hg/htdocs/contacts.html
- lines changed 3, context: html, text, full: html, text
added link to PLoS article on how to get help from scientific communities
- src/hg/htdocs/goldenPath/help/GTF.html
- lines changed 7, context: html, text, full: html, text
Added a line referring users to the wiki article for converting from GenePred to GTF
- lines changed 7, context: html, text, full: html, text
Changed the order of the last three sentences
- lines changed 2, context: html, text, full: html, text
Changed the link to WUStL to a more recent page
- src/hg/htdocs/goldenPath/help/customTrackText.html
- lines changed 1, context: html, text, full: html, text
Feature #986 (VCF+tabix): link to vcf.html from help docs forcustom tracks and track hubs.
- lines changed 3, context: html, text, full: html, text
Feature #986 (VCF+tabix): Added VCF to FAQformat.
- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
- lines changed 22, context: html, text, full: html, text
Feature #986 (VCF+tabix): link to vcf.html from help docs forcustom tracks and track hubs.
- src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html
- lines changed 89, context: html, text, full: html, text
Adding help page for VCF track options in hgTrackUi.
- src/hg/htdocs/goldenPath/help/vcf.html
- lines changed 2, context: html, text, full: html, text
Updated VCF format spec URL to latest version.
- lines changed 13, context: html, text, full: html, text
Feature #986 (VCF+tabix): updated vcf.html w/new example files.
- src/hg/htdocs/images/euFlag.gif
- lines changed 0, context: html, text, full: html, text
adding icons to use with euroNode
- src/hg/htdocs/images/phylo/xenTro3_9way.png
- lines changed 0, context: html, text, full: html, text
initial diagram for xenTro3 9-way alignment
- src/hg/htdocs/images/usFlag.gif
- lines changed 0, context: html, text, full: html, text
adding icons to use with euroNode
- src/hg/inc/hdb.h
- lines changed 13, context: html, text, full: html, text
Adding back some changes that were previously lost ina failed effort to neatly go back, review the commits, and write a better commit message. With that said, (1) hdb.h, hdb.c, and utrFa.c were all revised to allow utrFa to take a user-specified path to the nib files rather than looking up the path in dbDb. This allowed me to run utrFa on the transcripts in the temporary staging directory for the new UCSC Genes build, before those transcripts were in hg19 (the temporary directory was not in dbDb, and probably shouldn't be). (2) Copied some code from hg19.txt (thanks, Fan) to generate the keggPathway table. The previous code missed a lot of associations: since making this change, keggPathway has grown from about 9K to 60K lines
- src/hg/inc/mdb.h
- lines changed 8, context: html, text, full: html, text
Added in '-or' and ' || ' support to mdbPrint/mdbUpdate selections
- src/hg/js/jquery.tablednd.js
- lines changed 2, context: html, text, full: html, text
UCSC specific mods to table DnD broke subtrack DnD. Now fixed. Redmine 5494
- src/hg/lib/hdb.c
- lines changed 38, context: html, text, full: html, text
Adding back some changes that were previously lost ina failed effort to neatly go back, review the commits, and write a better commit message. With that said, (1) hdb.h, hdb.c, and utrFa.c were all revised to allow utrFa to take a user-specified path to the nib files rather than looking up the path in dbDb. This allowed me to run utrFa on the transcripts in the temporary staging directory for the new UCSC Genes build, before those transcripts were in hg19 (the temporary directory was not in dbDb, and probably shouldn't be). (2) Copied some code from hg19.txt (thanks, Fan) to generate the keggPathway table. The previous code missed a lot of associations: since making this change, keggPathway has grown from about 9K to 60K lines
- lines changed 1, context: html, text, full: html, text
Added a define back in that was accidentally removed.
- src/hg/lib/mdb.c
- lines changed 10, context: html, text, full: html, text
Made things a little less awkward for deleting vars
- lines changed 3, context: html, text, full: html, text
Added in '-or' and ' || ' support to mdbPrint/mdbUpdate selections
- src/hg/lib/vcfUi.c
- lines changed 5, context: html, text, full: html, text
Feature #3710 (vcfTabix UI): make sure link to hgVcfTrackHelp.htmlappears when boxed=TRUE in vcfCfgUi (already there for boxed=FALSE).
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release1.notes
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUncBsuProt.release1.notes
- lines changed 13, context: html, text, full: html, text
updated notes files for unc bsu prot
- src/hg/makeDb/doc/hg18.txt
- lines changed 19, context: html, text, full: html, text
Track #1656 (GWAS Catalog): bi-monthly update.
- src/hg/makeDb/doc/hg19.txt
- lines changed 107, context: html, text, full: html, text
new hgPal downloads for new knownGene
- lines changed 7, context: html, text, full: html, text
Track #1656 (GWAS Catalog): bi-monthly update.
- src/hg/makeDb/doc/melGal1.txt
- lines changed 60, context: html, text, full: html, text
rerun xenTro3 lastz with parameters that produce a bit more coverage
- src/hg/makeDb/doc/proteins/101005.txt
- lines changed 2, context: html, text, full: html, text
Updated the documentation in the build script to indicate the tables used only by the proteome browser (thanks, Fan)
- src/hg/makeDb/doc/rn4.txt
- lines changed 7, context: html, text, full: html, text
Added a correction step to fixwq rgdGene2Ensembl table.
- lines changed 51, context: html, text, full: html, text
add CDS FASTA alignments from rgdGene2 to downloads
- src/hg/makeDb/doc/sacCer3.txt
- lines changed 2, context: html, text, full: html, text
note about phyloBoot never finishing
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
- lines changed 34, context: html, text, full: html, text
Adding back some changes that were previously lost ina failed effort to neatly go back, review the commits, and write a better commit message. With that said, (1) hdb.h, hdb.c, and utrFa.c were all revised to allow utrFa to take a user-specified path to the nib files rather than looking up the path in dbDb. This allowed me to run utrFa on the transcripts in the temporary staging directory for the new UCSC Genes build, before those transcripts were in hg19 (the temporary directory was not in dbDb, and probably shouldn't be). (2) Copied some code from hg19.txt (thanks, Fan) to generate the keggPathway table. The previous code missed a lot of associations: since making this change, keggPathway has grown from about 9K to 60K lines
- src/hg/makeDb/doc/xenTro3.txt
- lines changed 243, context: html, text, full: html, text
repeat the melGal1 alignment and start the 9-way
- lines changed 206, context: html, text, full: html, text
have 9-way multiz with gene and gap annotations
- lines changed 122, context: html, text, full: html, text
done with 4D site tree estimate
- lines changed 248, context: html, text, full: html, text
phastCons done for 9-way
- lines changed 256, context: html, text, full: html, text
phyloP done for 9-way and working on downloads
- lines changed 4, context: html, text, full: html, text
done with 9-way alignment
- lines changed 55, context: html, text, full: html, text
added CDS FASTA alignments for ensGene
- src/hg/makeDb/mdbUpdate/mdbPrint.c
- lines changed 72, context: html, text, full: html, text
Added in '-or' and ' || ' support to mdbPrint/mdbUpdate selections
- src/hg/makeDb/mdbUpdate/mdbUpdate.c
- lines changed 1, context: html, text, full: html, text
Made things a little less awkward for deleting vars
- lines changed 47, context: html, text, full: html, text
Added in '-or' and ' || ' support to mdbPrint/mdbUpdate selections
- src/hg/makeDb/schema/all.joiner
- lines changed 6, context: html, text, full: html, text
Added a relationship between the tRNAName field in kgXref and the name field in the tRNAs table
- lines changed 2, context: html, text, full: html, text
Updated with some rgdGene2 entries.
- lines changed 1, context: html, text, full: html, text
Some update for rn4 rgdGene2.
- lines changed 4, context: html, text, full: html, text
Updated some entries to cover more rn4 rgdGene2 related IDs.
- lines changed 8, context: html, text, full: html, text
Build geneReviews to kgXref.genesymbol relationship
- src/hg/makeDb/trackDb/cow/bosTau2/gold.html
- src/hg/makeDb/trackDb/cow/bosTau6/gap.html
- lines changed 2, context: html, text, full: html, text
Added a period to the end of all bullet points
- src/hg/makeDb/trackDb/cow/bosTau6/trackDb.ra
- lines changed 16, context: html, text, full: html, text
add search rules for gold and ctgPos2
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 77, context: html, text, full: html, text
Adding 5 approved antibodies for Flo
- lines changed 6, context: html, text, full: html, text
There was a term where there should have been a type and adding a label
- lines changed 15, context: html, text, full: html, text
Adding new version for mapAlgorithm
- lines changed 8, context: html, text, full: html, text
Restored items lots from commit f29e7c395ee0c68912b3b4687a0b49cc3aa6e57a by commit 4df674dc20e935ce620b3c0603fe40008bbddeb3.
- lines changed 8, context: html, text, full: html, text
put back in lines whose deletion broke things, corrected searchable term in dccRep
- lines changed 9, context: html, text, full: html, text
corrected incorrect lab name for antibodies registered.
- lines changed 24, context: html, text, full: html, text
Adding Cell Lines and Antibodies
- lines changed 8, context: html, text, full: html, text
Adding Antibody Documents
- lines changed 5, context: html, text, full: html, text
added in goat control entry
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 528, context: html, text, full: html, text
Updates to cv from alpha
- src/hg/makeDb/trackDb/gap.html
- lines changed 1, context: html, text, full: html, text
Added a period to the end of all bullet points
- src/hg/makeDb/trackDb/human/hg19/knownGene.html
- lines changed 2, context: html, text, full: html, text
added missing closing bracket
- lines changed 1, context: html, text, full: html, text
Fixed an HTML error that left much of the methods section represented as a hyperlink
- lines changed 39, context: html, text, full: html, text
Put back the old content of knownGene.html. Moved the new content to knownGeneNew.html
- src/hg/makeDb/trackDb/human/hg19/knownGeneNew.html
- lines changed 156, context: html, text, full: html, text
Put back the old content of knownGene.html. Moved the new content to knownGeneNew.html
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
- lines changed 1162, context: html, text, full: html, text
added new tracks to broad histone metaDb
- lines changed 259, context: html, text, full: html, text
loaded 2 new borad tracks
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 682, context: html, text, full: html, text
See issue 2019, adding in some expIds, some labExpIds, working with the Myocyte issue
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
- lines changed 689, context: html, text, full: html, text
Changing file names to have Replicate
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra
- lines changed 859, context: html, text, full: html, text
added new tracks to Haib methyl 450
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 2003, context: html, text, full: html, text
added a lot of haib tfbs tracks
- lines changed 1184, context: html, text, full: html, text
added in new haib tracks
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
- lines changed 336, context: html, text, full: html, text
added in new tracks for open chrom chip
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
- lines changed 451, context: html, text, full: html, text
added in new entries for open chrom dnase
- lines changed 118, context: html, text, full: html, text
added one track to open chrom dnase
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
- lines changed 257, context: html, text, full: html, text
loaded 2 new tracks for sydh Histone
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 1409, context: html, text, full: html, text
loaded new tracks into release 2 sydh TFBS
- lines changed 7, context: html, text, full: html, text
last second revoke and replace of an experiment
- lines changed 31, context: html, text, full: html, text
corrected controls and long labels for replacement experiment
- lines changed 23, context: html, text, full: html, text
added bai's to fileName field.
- lines changed 54, context: html, text, full: html, text
renamed K562/SetDb1/UCD to be consistent with the other objects in the experiment
- lines changed 65, context: html, text, full: html, text
added new control to sydh tfbs
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUchicagoTfbs.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
- lines changed 75, context: html, text, full: html, text
Adding submissions 4771-4775 into a release2
- lines changed 5, context: html, text, full: html, text
removed erroneous origAsembly hg19 term
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProtFasp.ra
- lines changed 40, context: html, text, full: html, text
Adding the metaData for UncBsuProtFasp
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
- lines changed 1277, context: html, text, full: html, text
added a lot of uw tracks
- lines changed 813, context: html, text, full: html, text
added a lot of DGF tracks
- lines changed 108, context: html, text, full: html, text
removed random accession=hg19 fields
- lines changed 108, context: html, text, full: html, text
removed origAssembly from DGF
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
- lines changed 70, context: html, text, full: html, text
restored missing metadata
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
- lines changed 1, context: html, text, full: html, text
staging GIS RNA PET, redmine# 42
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGisRnaPet.ra
- lines changed 3550, context: html, text, full: html, text
staging GIS RNA PET, redmine# 42
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhTfbs.ra
- lines changed 3975, context: html, text, full: html, text
moving the updated metaDb for SYDH TFBS, redmine# 69
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUncBsuProt.ra
- lines changed 83, context: html, text, full: html, text
staging metadata for two new subtracks on beta, redmine 141
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
- lines changed 1, context: html, text, full: html, text
preparing to release UNC/BSU ProtGeno, redmine 141
- lines changed 1, context: html, text, full: html, text
Releasing HAIB Methyl RRBS (release 2), redmine# 2254
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibMethylRrbs.ra
- lines changed 9884, context: html, text, full: html, text
Releasing HAIB Methyl RRBS (release 2), redmine# 2254
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUncBsuProt.ra
- lines changed 306, context: html, text, full: html, text
preparing to release UNC/BSU ProtGeno, redmine 141
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 1, context: html, text, full: html, text
add python to this skunkworks alignment
- lines changed 50, context: html, text, full: html, text
Setting out to support two versions of the UCSC Genes details page: the old one on beta and RR, and a new one on alpha only. Trying to achieve this with two new trackDb.ra stanzas for knownGene (one for beta and RR, one for alpha), which should override the stanza in trackDb/trackDb.ra for hg19 only
- lines changed 1, context: html, text, full: html, text
Just learned that when you use the html qualifier, you shouldn't list your html filename with the html suffix
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 3, context: html, text, full: html, text
Adding submissions 4771-4775 into a release2
- lines changed 1, context: html, text, full: html, text
changed alpha to .new.ra for sydh tfbs
- lines changed 1, context: html, text, full: html, text
put it back to the .ra for sydh tfbs
- lines changed 2, context: html, text, full: html, text
enabling .ra to work on beta and alpha since it now contains the changes (2 new subtracks) that the .new.ra file had, redmine 141
- lines changed 2, context: html, text, full: html, text
Releasing HAIB Methyl RRBS (release 2), redmine# 2254
- lines changed 1, context: html, text, full: html, text
staging GIS RNA PET, redmine# 42
- lines changed 2, context: html, text, full: html, text
alpha, beta, public on sydh TFBS trackDb
- lines changed 2, context: html, text, full: html, text
Adding the release 2 structure and taking out the view level
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.new.ra
- lines changed 1, context: html, text, full: html, text
inserted new antibody terms
- lines changed 41, context: html, text, full: html, text
loaded 2 new borad tracks
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.html
- lines changed 1, context: html, text, full: html, text
See issue 2019, adding in some expIds, some labExpIds, working with the Myocyte issue
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra
- lines changed 9, context: html, text, full: html, text
See issue 2019, adding in some expIds, some labExpIds, working with the Myocyte issue
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.html
- lines changed 28, context: html, text, full: html, text
fixed html errors for GIS RNA PET, redmine# 42
- lines changed 17, context: html, text, full: html, text
Issue 42, adding the multiview instructions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
- lines changed 6, context: html, text, full: html, text
Many small changes for issue 42 for Vanessa
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra
- lines changed 353, context: html, text, full: html, text
added new tracks to Haib methyl 450
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.html
- lines changed 122, context: html, text, full: html, text
Releasing HAIB Methyl RRBS (release 2), redmine# 2254
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.html
- lines changed 65, context: html, text, full: html, text
Fixed typos, fixed html errors and rephrased sentences to avoid the use of the word we for HAIB Methyl RRBS, redmine# 2254
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra
- lines changed 1246, context: html, text, full: html, text
Releasing HAIB Methyl RRBS (release 2), redmine# 2254
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.new.ra
- lines changed 381, context: html, text, full: html, text
added a lot of haib tfbs tracks
- lines changed 1, context: html, text, full: html, text
changed alpha to html character code
- lines changed 231, context: html, text, full: html, text
added in new haib tracks
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.new.ra
- lines changed 57, context: html, text, full: html, text
added in new tracks for open chrom chip
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.new.ra
- lines changed 98, context: html, text, full: html, text
added in new entries for open chrom dnase
- lines changed 6, context: html, text, full: html, text
added in missing no treatments
- lines changed 25, context: html, text, full: html, text
added one track to open chrom dnase
- lines changed 3, context: html, text, full: html, text
added in missing non treatment
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.ra
- lines changed 4, context: html, text, full: html, text
Trying to add the pValue filters
- lines changed 2, context: html, text, full: html, text
Getting rid of minGreyLevel as it is not working properly
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.new.ra
- lines changed 44, context: html, text, full: html, text
loaded 2 new tracks for sydh Histone
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra
- lines changed 17, context: html, text, full: html, text
long labels for sydh tfbs
- lines changed 1, context: html, text, full: html, text
added time to EtOH 36Hr treatment. We should consider adding this to the cv, as that term is inconsistent with the others.
- lines changed 30, context: html, text, full: html, text
objects that needed to be pushed got pushed to release2, uncomment this later
- lines changed 278, context: html, text, full: html, text
loaded new tracks into release 2 sydh TFBS
- lines changed 3, context: html, text, full: html, text
updated the info on a replaced track
- lines changed 11, context: html, text, full: html, text
added new control to sydh tfbs
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
- lines changed 184, context: html, text, full: html, text
merged non-released release1 with the WIP release2 to be the new release 1
- lines changed 56, context: html, text, full: html, text
removed bad experiments after once-over
- lines changed 34, context: html, text, full: html, text
last second revoke and replace of an experiment
- lines changed 2, context: html, text, full: html, text
corrected controls and long labels for replacement experiment
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.new.ra
- lines changed 3, context: html, text, full: html, text
Adding submissions 4771-4775 into a release2
- lines changed 1, context: html, text, full: html, text
changing 'nuclear' in a long label to 'nucleus' to be consistent with its shortLabel and other nucleus localization subtrack longLabel, redmine 141
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra
- lines changed 20, context: html, text, full: html, text
copying .new.ra version over .ra to incorporate new subtracks, redmine #141
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtFasp.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.new.html
- lines changed 71, context: html, text, full: html, text
Adding the release 2 structure and taking out the view level
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.new.ra
- lines changed 1255, context: html, text, full: html, text
Adding the release 2 structure and taking out the view level
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra
- lines changed 441, context: html, text, full: html, text
added a lot of uw tracks
- lines changed 281, context: html, text, full: html, text
added a lot of DGF tracks
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.html
- lines changed 14, context: html, text, full: html, text
changed html for uw histone
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
- lines changed 263, context: html, text, full: html, text
fixed long labels UwHistone
- lines changed 425, context: html, text, full: html, text
fixed longlabels in uwtfbs, added in treatments in uw histone tfbs and cleanup
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
- lines changed 328, context: html, text, full: html, text
fixed longlabels in uwtfbs, added in treatments in uw histone tfbs and cleanup
- lines changed 236, context: html, text, full: html, text
short labels for uw tfbs
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 13, context: html, text, full: html, text
put back logic to handle geneReviews track using the geneReviews table in the database
- lines changed 12, context: html, text, full: html, text
Remove geneReviewsBB which is using wiki for update
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
- lines changed 452, context: html, text, full: html, text
Added 3 submissions, one of which replaced an old submission 3039.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
- lines changed 845, context: html, text, full: html, text
Added 3 more submissions.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 804, context: html, text, full: html, text
Added 6 new submissions for new release 3. Updated new.ra and trackDb.wgEncode.ra to have release 3 data showing on dev.
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
Added 6 new submissions for new release 3. Updated new.ra and trackDb.wgEncode.ra to have release 3 data showing on dev.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
- lines changed 87, context: html, text, full: html, text
Added 3 submissions, one of which replaced an old submission 3039.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
- lines changed 55, context: html, text, full: html, text
Added 3 more submissions.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.new.ra
- lines changed 888, context: html, text, full: html, text
Updated name of file to be in line with other new.ra files.
- lines changed 189, context: html, text, full: html, text
Added 6 new submissions for new release 3. Updated new.ra and trackDb.wgEncode.ra to have release 3 data showing on dev.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra
- lines changed 888, context: html, text, full: html, text
Updated name of file to be in line with other new.ra files.
- src/hg/makeDb/trackDb/oreganno.html
- lines changed 13, context: html, text, full: html, text
Redid the Display Conventions section to make it much easier to see what the colors mean ... as before they were buried in a paragraph with no color cues. I put a white backgound on it because the light green was almost impossible to read on the yellow background. It'sstill faint on the whote, but much better.
- lines changed 3, context: html, text, full: html, text
Added a little hack so that the box would expand/contract with font size and also work in IE7
- src/hg/makeDb/trackDb/sacCer/sacCer3/sgdGene.html
- lines changed 14, context: html, text, full: html, text
Cleaned up the html and rearranged text to make more sense and increase readability.
- lines changed 1, context: html, text, full: html, text
Added the word accessed for clarity and match the other sgd track.
- src/hg/makeDb/trackDb/sacCer/sacCer3/sgdOther.html
- lines changed 2, context: html, text, full: html, text
Fixe dtwo errors per code review #5470: corrected end p tag missing / and sentence missing a period.
- src/hg/makeDb/trackDb/turkey/melGal1/gap.html
- lines changed 1, context: html, text, full: html, text
Added a period to the end of all bullet points
- src/hg/makeDb/trackDb/windowmaskerSdust.html
- lines changed 1, context: html, text, full: html, text
Removed the 's' from 'sequence'
- src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html
- lines changed 400, context: html, text, full: html, text
initial contents copied from anoCar2 and updated for xenTro3
- src/hg/makeDb/trackDb/xenTro/xenTro3/trackDb.ra
- src/hg/rnaStructure/utrFa/utrFa.c
- lines changed 13, context: html, text, full: html, text
Adding back some changes that were previously lost ina failed effort to neatly go back, review the commits, and write a better commit message. With that said, (1) hdb.h, hdb.c, and utrFa.c were all revised to allow utrFa to take a user-specified path to the nib files rather than looking up the path in dbDb. This allowed me to run utrFa on the transcripts in the temporary staging directory for the new UCSC Genes build, before those transcripts were in hg19 (the temporary directory was not in dbDb, and probably shouldn't be). (2) Copied some code from hg19.txt (thanks, Fan) to generate the keggPathway table. The previous code missed a lot of associations: since making this change, keggPathway has grown from about 9K to 60K lines
- src/hg/utils/refSeqGet/refSeqGet.c
- lines changed 4, context: html, text, full: html, text
data status to metadata TSV
- src/hg/utils/refSeqGet/tests/expected/basicListTest.meta
- lines changed 6, context: html, text, full: html, text
data status to metadata TSV
- src/hg/utils/refSeqGet/tests/expected/versionedListTest.meta
- lines changed 4, context: html, text, full: html, text
data status to metadata TSV
- src/utils/bedToBigBed/bedToBigBed.c
- lines changed 1, context: html, text, full: html, text
fix per Jim.. a more clear usage message
- src/utils/qa/checkGbdbDiffs.csh
- lines changed 3, context: html, text, full: html, text
Got rid of annoying rm error with a hacky redirect to /dev/null.
- src/utils/qa/doGenbankTests
- lines changed 2, context: html, text, full: html, text
Implicating Brian in addition to Mark for gbSanity problems.
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 48610
- files changed: 231