All File Changes
v243_base to v244_preview (2010-11-02 to 2010-11-16) v244
- src/hg/encode/DAFs/2.0/caltechRnaSeq.daf
- lines changed 51, context: html, text, full: html, text
Changed DAF to display gtf files and to take different views based on GENCODE version
- src/hg/encode/DAFs/2.0/psuMm95c.daf
- lines changed 2, context: html, text, full: html, text
Updated the DAF's to include new lab name for Haridson Mouse Grants
- src/hg/encode/DAFs/2.0/psuMm9DnaseSeq.daf
- lines changed 2, context: html, text, full: html, text
Updated the DAF's to include new lab name for Haridson Mouse Grants
- src/hg/encode/DAFs/2.0/psuMm9Histone.daf
- lines changed 2, context: html, text, full: html, text
Updated the DAF's to include new lab name for Haridson Mouse Grants
- src/hg/encode/DAFs/2.0/psuMm9Tfbs.daf
- lines changed 2, context: html, text, full: html, text
Updated the DAF's to include new lab name for Haridson Mouse Grants
- src/hg/encode/DAFs/2.0/stanfordMm9Hist.daf
- lines changed 3, context: html, text, full: html, text
Updated DAF to take out strain requirement.
- src/hg/encode/DAFs/2.0/stanfordMm9Tfbs.daf
- lines changed 3, context: html, text, full: html, text
Updated DAF to take out strain requirement.
- src/hg/encode/encodeValidate/doEncodeValidate.pl
- lines changed 26, context: html, text, full: html, text
Validate daf lab and dataType. Remove obsolete parentTable.
- lines changed 2, context: html, text, full: html, text
changed fpkm1&2 type to fpkm, changed insDitrib to insDist as it is in the DAFs
- src/hg/encode/hgEncodeSubmit/app/controllers/pipeline_controller.rb
- lines changed 2, context: html, text, full: html, text
initial commit for separating out the archive expansion
- lines changed 12, context: html, text, full: html, text
adding expand as a separate background step
- src/hg/encode/hgEncodeSubmit/app/models/user.rb
- lines changed 10, context: html, text, full: html, text
adding permissions compensation for oddness of ftpasswd utility that wants to change perms to 444 if it can
- lines changed 2, context: html, text, full: html, text
needs rescue if not owner
- src/hg/encode/hgEncodeSubmit/app/views/pipeline/list.rhtml
- lines changed 16, context: html, text, full: html, text
adding expand as a separate background step
- src/hg/encode/hgEncodeSubmit/app/views/pipeline/show.rhtml
- lines changed 2, context: html, text, full: html, text
initial commit for separating out the archive expansion
- lines changed 4, context: html, text, full: html, text
adding expand as a separate background step
- src/hg/encode/hgEncodeSubmit/config/database.yml.sample
- lines changed 4, context: html, text, full: html, text
initial commit for separating out the archive expansion
- src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb
- lines changed 27, context: html, text, full: html, text
initial commit for separating out the archive expansion
- lines changed 61, context: html, text, full: html, text
adding expand as a separate background step
- lines changed 12, context: html, text, full: html, text
reducing duplicate project status messages in the log
- lines changed 2, context: html, text, full: html, text
cleaning up project.status for duplicate expanding messages
- src/hg/encode/hgEncodeSubmit/pipeline_runner.rb
- lines changed 21, context: html, text, full: html, text
initial commit for separating out the archive expansion
- src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
- lines changed 111, context: html, text, full: html, text
Added support for typOfTerm settings, allowing a table of contents of all important term types
- lines changed 12, context: html, text, full: html, text
Added special case for mouse cell lines link showing up in typeOfTerms TOC
- lines changed 17, context: html, text, full: html, text
Table of Grants needs to show grant Institution
- lines changed 6, context: html, text, full: html, text
Multiple protocols should appear on separate lines.
- src/hg/hgCustom/hgCustom.c
- lines changed 2, context: html, text, full: html, text
Typo. Changed Genomes to Genome.
- src/hg/hgGene/ctd.c
- lines changed 30, context: html, text, full: html, text
Update for RGD Genes, Redmine issue #29.
- src/hg/hgGene/hgGene.c
- lines changed 22, context: html, text, full: html, text
Update for RGD Genes, Redmine issue #29.
- src/hg/hgGene/hgGene.h
- lines changed 14, context: html, text, full: html, text
Update for RGD Genes, Redmine issue #29.
- src/hg/hgGene/links.c
- lines changed 7, context: html, text, full: html, text
Update for RGD Genes, Redmine issue #29.
- src/hg/hgGene/makefile
- lines changed 1, context: html, text, full: html, text
Update for RGD Genes, Redmine issue #29.
- src/hg/hgGene/pathways.c
- lines changed 63, context: html, text, full: html, text
Update for RGD Genes, Redmine issue #29.
- src/hg/hgGene/rgdInfo.c
- lines changed 330, context: html, text, full: html, text
Update for RGD Genes, Redmine issue #29.
- src/hg/hgGene/synonym.c
- lines changed 98, context: html, text, full: html, text
Update for RGD Genes, Redmine issue #29.
- src/hg/hgTables/hgTables.c
- lines changed 2, context: html, text, full: html, text
removed print of sql stats to stderr, which was there for debugging socket leak in hgTables
- src/hg/hgTrackUi/hgTrackUi.c
- src/hg/hgTracks/cds.c
- lines changed 30, context: html, text, full: html, text
support codon numbering in genePred tracks
- src/hg/hgTracks/cds.h
- lines changed 1, context: html, text, full: html, text
support codon numbering in genePred tracks
- src/hg/hgTracks/config.c
- lines changed 6, context: html, text, full: html, text
Added support for pennantIcon as requested by b0b. First use flagging hg18 to hg19 liftOver tracks.
- src/hg/hgTracks/hgTracks.c
- lines changed 10, context: html, text, full: html, text
Found recursive loop that wigMafs fell into with rightClick. The particular code may not actually be needed and has been ifdef'd OMITted.
- lines changed 16, context: html, text, full: html, text
Fixed bug 32 in 1071. Repeated vis changes in track search had unpredictable consequences.
- lines changed 66, context: html, text, full: html, text
Added support for pennantIcon as requested by b0b. First use flagging hg18 to hg19 liftOver tracks.
- lines changed 7, context: html, text, full: html, text
Simultaneous reshaping and composite cleanup no longer conflict if reshaping goes first.
- src/hg/hgTracks/hgTracks.h
- lines changed 1, context: html, text, full: html, text
support codon numbering in genePred tracks
- src/hg/hgTracks/imageV2.h
- src/hg/hgTracks/searchTracks.c
- lines changed 1, context: html, text, full: html, text
strip-out double quotes from description search string
- src/hg/hgTracks/simpleTracks.c
- lines changed 4, context: html, text, full: html, text
Don't trust freq column to have data or to match the allele count, handle blank, error on mismatch
- lines changed 1, context: html, text, full: html, text
Fix for useScore and strand for bed detail (with bed6). Issue 1642 in redmine.
- lines changed 40, context: html, text, full: html, text
some cactus stuff for benedict
- lines changed 1, context: html, text, full: html, text
Work in progress for #559: split snp131 into 3 subtracks:Common: uniquely mapped SNPs found by HapMap and/or 1000 Genomes;
Misc: uniquely mapped SNPs;
Non-unique: SNPs that map to more than one genomic location.
Currently I'm only using the validation codes by-hapmap and
by-1000genomes to separate Common and Misc; however, I really
should add a filter on allele frequency because the dbSNP doc
implies that some by-hapmap SNPs only found a single allele,
which would mean they validated that it's not a common SNP.
We don't get allele freq data from dbSNP; would need to fetch
new db dump files etc. It would be great to include allele
freq data in the SNPs track if we go to the trouble, and Jim
has suggested adding a clinically associated bit (although
that bit can be triggered by the most tangential of associations,
like region endpoints in OMIM). Spot-checking other validation
codes, none of them seem reliable enough to use as a basis for
Common. E.g. cluster might be from earlier+later version of same
submitter's bulk submission.
- lines changed 5, context: html, text, full: html, text
support codon numbering in genePred tracks
- lines changed 1, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): work in progress: basic tables areloaded (snp132, snp132Exceptions, snp132ExceptionDesc, snp132Seq).
Still need to build ortho alleles, snp132CodingDbSnp; still
need to split up snp132 into subsets which will end up either as
subtracks or individual tracks, TBD; and still need to add new
columns for allele frequency & bitfields (or at least the clinically
assoc'd bit).
- lines changed 1, context: html, text, full: html, text
support codon numbering checkbox in hgTrackUi
- src/hg/hgc/hgc.c
- lines changed 1, context: html, text, full: html, text
Added pgIrish track to pgSnp type hgc clicks
- src/hg/htdocs/ENCODE/dataStandards.html
- lines changed 5, context: html, text, full: html, text
enabling link to Data Standards from ENCODE portal; editing dataStandards page with correct link and title with slight edits to exlanation
- src/hg/htdocs/ENCODE/index.html
- lines changed 1, context: html, text, full: html, text
enabling link to Data Standards from ENCODE portal; editing dataStandards page with correct link and title with slight edits to exlanation
- lines changed 23, context: html, text, full: html, text
Added a news item on the OpenHelix ENCODE tutorial
- src/hg/htdocs/FAQ/FAQformat.html
- lines changed 2, context: html, text, full: html, text
Added db=hg19 to bedDetail example link to make it work when another db is in the cart, and added name and description to sample pgSnp data.
- lines changed 2, context: html, text, full: html, text
Fixed indels in pgSnp format. Thanks, Belinda. (redmine #1495)
- src/hg/htdocs/goldenPath/help/customTrackText.html
- lines changed 82, context: html, text, full: html, text
Removing bedDetail and pgSnp track types from this doc and just linking to their descriptions in FAQformat.html, as was decided in Redmine #1495
- src/hg/htdocs/goldenPath/help/hg18ToHg19LiftOver.html
- lines changed 41, context: html, text, full: html, text
added explanation page for 18-ball icon
- src/hg/htdocs/goldenPath/help/trackSearch.html
- lines changed 1, context: html, text, full: html, text
when Vanessa updated the file with new html standards, a bullet got added to the ENCODE terms section where I really just wanted an indent. This change removes the bullet
- src/hg/htdocs/goldenPath/pubs.html
- lines changed 6, context: html, text, full: html, text
Added cancer browser paper.
- src/hg/htdocs/images/18.jpg
- lines changed 0, context: html, text, full: html, text
icon for tracks lifted hg18 to hg19
- lines changed 0, context: html, text, full: html, text
added one pixel row at bottom for symmetry
- lines changed 0, context: html, text, full: html, text
added orange background to corners to match
- lines changed 0, context: html, text, full: html, text
changed to 16x16 pixels for cleaner look
- lines changed 0, context: html, text, full: html, text
hopefully final tweak. 16x16 with orange color in corners
- src/hg/htdocs/images/eye.png
- lines changed 0, context: html, text, full: html, text
New16x16 icon for rightClick view
- lines changed 0, context: html, text, full: html, text
Eye needs to be at the bottom, not the middle of the 16x16 png
- src/hg/inc/bedDetail.h
- lines changed 3, context: html, text, full: html, text
Added error checking for pgSnp and bedDetail custom track loaders, issue #1595
- src/hg/inc/hui.h
- lines changed 3, context: html, text, full: html, text
Added support for pennantIcon as requested by b0b. First use flagging hg18 to hg19 liftOver tracks.
- lines changed 1, context: html, text, full: html, text
support codon numbering checkbox in hgTrackUi
- src/hg/inc/mdb.h
- lines changed 4, context: html, text, full: html, text
Added support for getting cv typeOfTerms hash and made the cv whitelist ise cv.ra
- src/hg/inc/pgSnp.h
- lines changed 4, context: html, text, full: html, text
Added error checking for pgSnp and bedDetail custom track loaders, issue #1595
- src/hg/js/hgTracks.js
- lines changed 5, context: html, text, full: html, text
make sure openLink links contain chrom
- lines changed 19, context: html, text, full: html, text
add makeImgTag to fix FireFox problem
- lines changed 10, context: html, text, full: html, text
Support for AJAX callback at initial load to retrieve individual tracks. This is useful if a track has a remote data source and will take a long time to retrieve, then draw the image.
- src/hg/js/utils.js
- src/hg/lib/bedDetail.c
- lines changed 122, context: html, text, full: html, text
Added error checking for pgSnp and bedDetail custom track loaders, issue #1595
- src/hg/lib/cart.c
- lines changed 52, context: html, text, full: html, text
Fixed bug 32 in 1071. Repeated vis changes in track search had unpredictable consequences.
- lines changed 22, context: html, text, full: html, text
Fixed part of redmine 1071.35 where subtrack not selected is made visible. Also half of fix where selecting both composite and subtrack simultaneously will do composite cleanup but not subtrack shaping. That is, composite vis will override selected subtrack vis.
- src/hg/lib/customFactory.c
- lines changed 15, context: html, text, full: html, text
Added error checking for pgSnp and bedDetail custom track loaders, issue #1595
- lines changed 38, context: html, text, full: html, text
Changed errAborts to lineFileAborts so includes line number in error messages. Improved pgSnp recognizer so type is not required in track line(#1595).
- lines changed 5, context: html, text, full: html, text
Prevent pgSnpRecognizer from returning before calling customPpReuse(as Brooke noticed, this caused the first line to be lost for types
with recognizers that run after pgSnp).
- src/hg/lib/encode/chiaPet.as
- lines changed 12, context: html, text, full: html, text
autoSql file for chiaPet anchors and clusters
- src/hg/lib/encode/chiaPet.sql
- src/hg/lib/hgFind.c
- lines changed 6, context: html, text, full: html, text
Bug found by Fan: in our zeal to detect "term:offset" (e.g. "chr1:2385495")search terms, we were mangling IDs like "RGD:2138". Solution: don't support
single-base offsets except for sequences named in chromInfo
(hgOfficialChromName).
- lines changed 3, context: html, text, full: html, text
Better bug fix for b509f936321e0d635a785f48ee0638744fbc3b8d:chop up a copy, not the original search term, when it looks like
a chrom:offset or chrom:start-end term. Merely restoring the
original for searching left the original term chopped for
error-reporting, which meant a truncated term in the message
when a term couldn't be found, as Fan noticed.
- lines changed 21, context: html, text, full: html, text
Track #1570 (search using OMIM id used in URL): added support forsingleSearch=omimGeneAcc, or any searchName (which defaults to
searchTable if not defined in trackDb.ra). May not be strictly
necessary for OMIM because as Fan found OMIM numeric IDs already
get unique semiShortCircuit hits, but we expect this to be useful
for track-specific links to us in general.
- src/hg/lib/hui.c
- lines changed 50, context: html, text, full: html, text
The '...' metadata table now links to term definitions and specific cv defined terms
- lines changed 10, context: html, text, full: html, text
Fixed 1480 repoort of show stopper by Mary. mRNA checkboxes were not working.
- lines changed 1, context: html, text, full: html, text
Had to change tdbVisLimitedByAncestors, because it didn't handle subtracks where view or composite was not at default vis
- lines changed 36, context: html, text, full: html, text
Added support for pennantIcon as requested by b0b. First use flagging hg18 to hg19 liftOver tracks.
- lines changed 1, context: html, text, full: html, text
Removed an erroneous freeMem
- lines changed 9, context: html, text, full: html, text
support codon numbering checkbox in hgTrackUi
- src/hg/lib/mdb.c
- lines changed 122, context: html, text, full: html, text
Added support for getting cv typeOfTerms hash and made the cv whitelist ise cv.ra
- lines changed 5, context: html, text, full: html, text
Fixed bug where cell was not showing up in whitelist to track search
- src/hg/lib/pgSnp.c
- lines changed 37, context: html, text, full: html, text
Added error checking for pgSnp and bedDetail custom track loaders, issue #1595
- lines changed 3, context: html, text, full: html, text
Changed errAborts to lineFileAborts so includes line number in error messages. Improved pgSnp recognizer so type is not required in track line(#1595).
- src/hg/lib/rgdGene2ToDescription.sql
- src/hg/lib/rgdGene2Xref.sql
- src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt
- lines changed 146, context: html, text, full: html, text
Cricket noticed 15 fastqs missing. The update links 12 from hg18 but 3 remain for Broad to submit
- lines changed 652, context: html, text, full: html, text
Broad submitted hg19 peaks (finally) and resubmitted most bamsand bigWigs AND 3 missing fastqs
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeSunyAlbanyGeneSt.release1.notes
- lines changed 86, context: html, text, full: html, text
New notes file for SUNY Tiling
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeSunyAlbanyTiling.release1.notes
- lines changed 60, context: html, text, full: html, text
New notes file for SUNY Tiling
- src/hg/makeDb/doc/felCat4.txt
- src/hg/makeDb/doc/felCatV17e.txt
- src/hg/makeDb/doc/hg17.txt
- lines changed 14, context: html, text, full: html, text
Track #1702 (DGV update): need to update hg17 too (minimal changes).
- src/hg/makeDb/doc/hg18.txt
- lines changed 5, context: html, text, full: html, text
redmine bug #19 reload polyaDb
- lines changed 11, context: html, text, full: html, text
Track #1702 (DGV update): done in hg18 and hg19.
- src/hg/makeDb/doc/hg19.txt
- lines changed 8, context: html, text, full: html, text
redmine 1467 knownToU133Plus2 tracks
- lines changed 61, context: html, text, full: html, text
Work in progress for #559: split snp131 into 3 subtracks:Common: uniquely mapped SNPs found by HapMap and/or 1000 Genomes;
Misc: uniquely mapped SNPs;
Non-unique: SNPs that map to more than one genomic location.
Currently I'm only using the validation codes by-hapmap and
by-1000genomes to separate Common and Misc; however, I really
should add a filter on allele frequency because the dbSNP doc
implies that some by-hapmap SNPs only found a single allele,
which would mean they validated that it's not a common SNP.
We don't get allele freq data from dbSNP; would need to fetch
new db dump files etc. It would be great to include allele
freq data in the SNPs track if we go to the trouble, and Jim
has suggested adding a clinically associated bit (although
that bit can be triggered by the most tangential of associations,
like region endpoints in OMIM). Spot-checking other validation
codes, none of them seem reliable enough to use as a basis for
Common. E.g. cluster might be from earlier+later version of same
submitter's bulk submission.
- lines changed 8, context: html, text, full: html, text
Track #1702 (DGV update): done in hg18 and hg19.
- lines changed 429, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): work in progress: basic tables areloaded (snp132, snp132Exceptions, snp132ExceptionDesc, snp132Seq).
Still need to build ortho alleles, snp132CodingDbSnp; still
need to split up snp132 into subsets which will end up either as
subtracks or individual tracks, TBD; and still need to add new
columns for allele frequency & bitfields (or at least the clinically
assoc'd bit).
- src/hg/makeDb/doc/hg19Patch2.txt
- lines changed 14, context: html, text, full: html, text
fixup altSeqLiftOverPsl table to be proper psl
- src/hg/makeDb/doc/nomLeu1.txt
- src/hg/makeDb/doc/rheMac2.txt
- lines changed 8, context: html, text, full: html, text
fixed result of cascading yank and put error (renamed track to drop extra n)
- src/hg/makeDb/doc/rn4.txt
- lines changed 192, context: html, text, full: html, text
Updated build process of rn4 RGD Genes related build. Ticket #29.
- src/hg/makeDb/genbank/doc/to-do.txt
- lines changed 3, context: html, text, full: html, text
added problem case RefSeq NR to doc
- src/hg/makeDb/genbank/etc/align.dbs
- src/hg/makeDb/genbank/etc/genbank.conf
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- src/hg/makeDb/genbank/src/lib/gbGenome.c
- src/hg/makeDb/schema/all.joiner
- lines changed 1, context: html, text, full: html, text
adding metaDb to the tables ignored
- lines changed 17, context: html, text, full: html, text
adding hg19ContigDiff and ignoring metaDb
- lines changed 9, context: html, text, full: html, text
fixing rule for wgEncodeGencodeYalePseudoV4 and adding hg19Patch2 ext seqFile checks and altSeq table ignores for hg19
- lines changed 5, context: html, text, full: html, text
adding identifier hg18ContigDiff
- lines changed 6, context: html, text, full: html, text
redmine 386: Add NumtSeq tables to ignoredTables with hg18
- src/hg/makeDb/schema/joiner.doc
- lines changed 1, context: html, text, full: html, text
add note about dupeOk only on primary key
- src/hg/makeDb/trackDb/README
- lines changed 7, context: html, text, full: html, text
add information about itemRgb
- lines changed 9, context: html, text, full: html, text
add note about how to load a bigBed file
- lines changed 5, context: html, text, full: html, text
Added pennantIcon to README
- src/hg/makeDb/trackDb/buildTrix
- lines changed 2, context: html, text, full: html, text
not an error if database has no tables
- src/hg/makeDb/trackDb/cat/felCat4/trackDb.ra
- src/hg/makeDb/trackDb/cat/felCatV17e/ctgPos2.html
- src/hg/makeDb/trackDb/cat/felCatV17e/description.html
- src/hg/makeDb/trackDb/cat/felCatV17e/gap.html
- src/hg/makeDb/trackDb/cat/felCatV17e/gold.html
- src/hg/makeDb/trackDb/cat/felCatV17e/trackDb.ra
- src/hg/makeDb/trackDb/ccdsGene.html
- lines changed 5, context: html, text, full: html, text
Added some exceptions to criteria used to create CCDS annotations.
- src/hg/makeDb/trackDb/checkMetaDb
- lines changed 4, context: html, text, full: html, text
make a small change so that errors get propogated upstream
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 87, context: html, text, full: html, text
I have merged my labels with Tims for typeOfTerm, I still have the SpecialStory variables to check on
- lines changed 26, context: html, text, full: html, text
Adding labs CRG-Guigo and UCSC and grant UCSC as part of metaDb cleanup
- lines changed 26, context: html, text, full: html, text
Reviewed provisional changes relating to MDB terms
- lines changed 83, context: html, text, full: html, text
Added description fields to stanzas without them
- lines changed 36, context: html, text, full: html, text
Updated the Open Chromatin protocol label, as requested by Greg Crawford
- lines changed 12, context: html, text, full: html, text
Added PSU Mouse Lab type
- src/hg/makeDb/trackDb/human/agilentCghAlpha.html
- lines changed 49, context: html, text, full: html, text
Added two human Agilent arrays and updated alpha description/trackDb.
- src/hg/makeDb/trackDb/human/hg18/hg18ContigDiff.html
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadChipSeq.ra
- lines changed 372, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeChromatinMap.ra
- lines changed 527, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 25, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
- lines changed 55, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisDnaPet.ra
- lines changed 62, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisPet.ra
- lines changed 168, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisRnaSeq.ra
- lines changed 30, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHelicosRnaSeq.ra
- lines changed 1, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
- lines changed 343, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaCnv.ra
- lines changed 6, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeReg.ra
- lines changed 5, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- lines changed 5, context: html, text, full: html, text
Adding labs CRG-Guigo and UCSC and grant UCSC as part of metaDb cleanup
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeRikenCage.ra
- lines changed 101, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeSunyalbanyRnaGeneChip.ra
- lines changed 7, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- lines changed 0, context: html, text, full: html, text
releasing metaDb changes made by Tim; changing dataType to RipChip; also in alpha version removing space after RipChip
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwAffyExonArray.ra
- lines changed 71, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwChIPSeq.ra
- lines changed 822, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDGF.ra
- lines changed 36, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDnaseSeq.ra
- lines changed 163, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- lines changed 401, context: html, text, full: html, text
Forgot one instance of 'lab Uw' that should be 'lab UW'
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
- lines changed 278, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeBroadChipSeq.ra
- lines changed 372, context: html, text, full: html, text
releasing metaDb changes made by Tim; removed parentTable, which is no longer used as a metaDb term
- src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeChromatinMap.ra
- lines changed 527, context: html, text, full: html, text
releasing metaDb changes made by Tim; removed parentTable and changed FAIREseq to FaireSeq
- src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeCshlLongRnaSeq.ra
- lines changed 25, context: html, text, full: html, text
releasing metaDb changes made by Tim; changed cshl to CSHL
- src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeGisPet.ra
- lines changed 168, context: html, text, full: html, text
releasing metaDb changes made by Tim; removed parentTable and changed all lab to GIS
- src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeReg.ra
- lines changed 10, context: html, text, full: html, text
releasing metaDb changes made by Tim; changed lab from Kent to UCSC
- src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeRikenCage.ra
- lines changed 101, context: html, text, full: html, text
releasing metaDb changes made by Tim; removing parentTable and changing Riken to RIKEN
- src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeSunyalbanyRnaGeneChip.ra
- lines changed 7, context: html, text, full: html, text
releasing metaDb changes made by Tim; changing dataType to RipChip; also in alpha version removing space after RipChip
- src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeUwAffyExonArray.ra
- lines changed 71, context: html, text, full: html, text
releasing metaDb changes made by Tim; changing lab from Uw to UW
- src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeUwChIPSeq.ra
- lines changed 822, context: html, text, full: html, text
releasing metaDb changes made by Tim; removing parentTable and changing lab from Uw to UW
- src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeUwDGF.ra
- lines changed 36, context: html, text, full: html, text
releasing metaDb changes made by Tim; removing parentTable and changing lab from Uw to UW
- src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeUwDnaseSeq.ra
- lines changed 564, context: html, text, full: html, text
releasing metaDb changes made by Tim; removing parentTable and changing lab from Uw to UW
- src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeYaleChIPseq.ra
- lines changed 3511, context: html, text, full: html, text
staging and releasing metaDb clean-up Cricket did (Redmine Issue #1086)
- lines changed 278, context: html, text, full: html, text
releasing metaDb changes made by Tim; changing lab from Harvard(Struhl) to Harvard as well as UCD(Farnham) to UCD
- src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeBroadChipSeq.ra
- lines changed 372, context: html, text, full: html, text
releasing metaDb changes made by Tim; removed parentTable, which is no longer used as a metaDb term
- src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeChromatinMap.ra
- lines changed 527, context: html, text, full: html, text
releasing metaDb changes made by Tim; removed parentTable and changed FAIREseq to FaireSeq
- src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeCshlLongRnaSeq.ra
- lines changed 25, context: html, text, full: html, text
releasing metaDb changes made by Tim; changed cshl to CSHL
- src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeGisPet.ra
- lines changed 168, context: html, text, full: html, text
releasing metaDb changes made by Tim; removed parentTable and changed all lab to GIS
- src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeReg.ra
- lines changed 10, context: html, text, full: html, text
releasing metaDb changes made by Tim; changed lab from Kent to UCSC
- src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeRikenCage.ra
- lines changed 101, context: html, text, full: html, text
releasing metaDb changes made by Tim; removing parentTable and changing Riken to RIKEN
- src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeSunyalbanyRnaGeneChip.ra
- lines changed 7, context: html, text, full: html, text
releasing metaDb changes made by Tim; changing dataType to RipChip; also in alpha version removing space after RipChip
- src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeUwAffyExonArray.ra
- lines changed 71, context: html, text, full: html, text
releasing metaDb changes made by Tim; changing lab from Uw to UW
- src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeUwChIPSeq.ra
- lines changed 822, context: html, text, full: html, text
releasing metaDb changes made by Tim; removing parentTable and changing lab from Uw to UW
- src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeUwDGF.ra
- lines changed 36, context: html, text, full: html, text
releasing metaDb changes made by Tim; removing parentTable and changing lab from Uw to UW
- src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeUwDnaseSeq.ra
- lines changed 564, context: html, text, full: html, text
releasing metaDb changes made by Tim; removing parentTable and changing lab from Uw to UW
- src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeYaleChIPseq.ra
- lines changed 3511, context: html, text, full: html, text
staging and releasing metaDb clean-up Cricket did (Redmine Issue #1086)
- lines changed 278, context: html, text, full: html, text
releasing metaDb changes made by Tim; changing lab from Harvard(Struhl) to Harvard as well as UCD(Farnham) to UCD
- src/hg/makeDb/trackDb/human/hg18/numtSeq.html
- lines changed 47, context: html, text, full: html, text
Move up one level to trackDb/human
- src/hg/makeDb/trackDb/human/hg18/pgSnp.html
- lines changed 160, context: html, text, full: html, text
Work in progress for Track #683: moving almost all of Belinda'sGenome Variants hgwdev-only subtracks into the main Genome Variants.
Also updating some reference links and adding subtrack matrix settings.
- lines changed 6, context: html, text, full: html, text
Removed a bit of pubmed link cruft.
- lines changed 18, context: html, text, full: html, text
Track #683: Moving the new pgIrish from pgSnpHgwdev to pgSnp.
- src/hg/makeDb/trackDb/human/hg18/pgSnpHgwdev.html
- lines changed 14, context: html, text, full: html, text
adding irish snps to genome variants
- src/hg/makeDb/trackDb/human/hg18/trackDb.ra
- lines changed 15, context: html, text, full: html, text
Work in progress for Track #683: moving almost all of Belinda'sGenome Variants hgwdev-only subtracks into the main Genome Variants.
Also updating some reference links and adding subtrack matrix settings.
- src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.html
- lines changed 2, context: html, text, full: html, text
made changes that were requested in a code review
- lines changed 8, context: html, text, full: html, text
changing display to explain U and D, issue#1206
- src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.ra
- lines changed 140, context: html, text, full: html, text
changing display to explain U and D, issue#1206
- src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.new.ra
- lines changed 721, context: html, text, full: html, text
removing a copy of wgEncodeRikenCage.ra
- src/hg/makeDb/trackDb/human/hg19/hg19ContigDiff.html
- lines changed 4, context: html, text, full: html, text
changing wording and spacing
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
- lines changed 12, context: html, text, full: html, text
Changed some antibodies from 'Input' to 'Control' for uniformity
- lines changed 241, context: html, text, full: html, text
Added 12 more fastq's as links to hg18
- lines changed 529, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- lines changed 473, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- lines changed 3544, context: html, text, full: html, text
Resubmission of almost all Broad hg19 and new submission of peaks and a couple missing fastq
- lines changed 14, context: html, text, full: html, text
Removed parentTables that snuck back in
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 77, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 165, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- lines changed 481, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
- lines changed 11, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- lines changed 15, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra
- lines changed 28, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- lines changed 4, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
- lines changed 81, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- lines changed 639, context: html, text, full: html, text
added the fastqs from hg18
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra
- lines changed 6, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- lines changed 19, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
- lines changed 108, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- lines changed 14, context: html, text, full: html, text
Change protocol from 'HudsoneAlpha' to 'HAIB-p1' to avoid term conflict with lab 'HidsonAlpha'
- lines changed 286, context: html, text, full: html, text
Added submissions 2471. Changed view back to normal 2-D Matrix view
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
- lines changed 44, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- lines changed 119, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 719, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- lines changed 17, context: html, text, full: html, text
As long as mdbs are being cleaned up... removed some labVersions which were duplicate with labExpId
- lines changed 91, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- lines changed 4847, context: html, text, full: html, text
Added 16 submissions of Signal data
- lines changed 666, context: html, text, full: html, text
Added 4 submissions that were stuck in the submit q
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
- lines changed 333, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- lines changed 52, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- lines changed 137, context: html, text, full: html, text
Added one submission to Open Chrom ChIPSeq Data
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
- lines changed 129, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- lines changed 43, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- lines changed 667, context: html, text, full: html, text
Added 6 submissions to trackDb
- lines changed 1426, context: html, text, full: html, text
added fastqs from hg18
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
- lines changed 203, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- lines changed 38, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- lines changed 812, context: html, text, full: html, text
Added 2 submissions to Faire-seq track
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
- lines changed 20, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- lines changed 199, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
- lines changed 52, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- lines changed 7, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 669, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- lines changed 43, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- lines changed 8828, context: html, text, full: html, text
added fastqs from hg18
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
- lines changed 112, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- lines changed 113, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
- lines changed 19, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- lines changed 43, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 153, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- lines changed 201, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
- lines changed 310, context: html, text, full: html, text
Added 3 submissions to the trackDb and metaDb
- lines changed 870, context: html, text, full: html, text
Fixed some missing data and display issues
- lines changed 278, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- lines changed 343, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- lines changed 4, context: html, text, full: html, text
Updated origAssembly tag for tracks lifted from hg18
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
- lines changed 4728, context: html, text, full: html, text
Added 49 submissions for UW TFBS
- lines changed 76, context: html, text, full: html, text
Fixed some missing data and display issues
- lines changed 384, context: html, text, full: html, text
Cleaned up unregistered labs and dataTypes. Removed parentTable.
- lines changed 200, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeYaleRnaSeq.ra
- lines changed 13, context: html, text, full: html, text
removed the post ENCODE June Freeze tag
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
- lines changed 1, context: html, text, full: html, text
staging UWDNase on hgwbeta
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDnase.ra
- lines changed 9463, context: html, text, full: html, text
staging UWDNase on hgwbeta
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 1, context: html, text, full: html, text
improved regex for ctgPos2 search
- lines changed 2, context: html, text, full: html, text
termRegex fixup for ctgPos2
- lines changed 53, context: html, text, full: html, text
Added entry for a second run of RetroFinder on hg19. Added searches for the track.
- lines changed 1, context: html, text, full: html, text
added liftOver from hg18 icon to snp130
- lines changed 1, context: html, text, full: html, text
changed O in liftOver for snp130 pennantIcon call to capital to match actual filename
- lines changed 11, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): work in progress: basic tables areloaded (snp132, snp132Exceptions, snp132ExceptionDesc, snp132Seq).
Still need to build ortho alleles, snp132CodingDbSnp; still
need to split up snp132 into subsets which will end up either as
subtracks or individual tracks, TBD; and still need to add new
columns for allele frequency & bitfields (or at least the clinically
assoc'd bit).
- src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.html
- lines changed 1, context: html, text, full: html, text
Made the data reference plural.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.ra
- lines changed 34, context: html, text, full: html, text
turned the default settings to off for Transfrags
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.ra
- lines changed 1354, context: html, text, full: html, text
Added all but one peak tracks. Reorganized a little bit.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.html
- lines changed 2, context: html, text, full: html, text
changed Gerlad to GERALD and removed artifactually
- lines changed 2, context: html, text, full: html, text
making changes per Vanessa's code reivew feedback: added # in front of hex color values and changed hgdownload-test.cse to hgdownload
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.ra
- lines changed 2, context: html, text, full: html, text
removed the grey shading option for Transfrags Issue#44Item#68
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
- lines changed 3, context: html, text, full: html, text
changed visibility settings
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.html
- lines changed 2, context: html, text, full: html, text
removed read score formula since the labs say it is irrelevant
- lines changed 5, context: html, text, full: html, text
changed spelling errors and added a sam tools reference
- lines changed 2, context: html, text, full: html, text
added information about the custom tags
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra
- lines changed 1, context: html, text, full: html, text
changed bam setting to color by strand
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.html
- lines changed 153, context: html, text, full: html, text
Updated Track Description and Configuration to match hg18
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra
- lines changed 6, context: html, text, full: html, text
Updated Track Description and Configuration to match hg18
- lines changed 1, context: html, text, full: html, text
Fixed typo in spelling HTC-116
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRrbs.ra
- lines changed 1, context: html, text, full: html, text
Removed tag that replicates Growth Protocol for variables under term growth protocol
- lines changed 1, context: html, text, full: html, text
fixed the spelling mistake of Treatment
- lines changed 1, context: html, text, full: html, text
Added Updated the label tag for where cells were obtained at.
- lines changed 143, context: html, text, full: html, text
Added submissions 2471. Changed view back to normal 2-D Matrix view
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.html
- lines changed 104, context: html, text, full: html, text
Updated track description with changes provided by the lab
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
- lines changed 1692, context: html, text, full: html, text
Added 16 submissions of Signal data
- lines changed 1, context: html, text, full: html, text
Fixed trackDb with noInherit on
- lines changed 219, context: html, text, full: html, text
Added 4 submissions that were stuck in the submit q
- lines changed 1, context: html, text, full: html, text
Updated Track configuration page
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra
- lines changed 27, context: html, text, full: html, text
Added one submission to Open Chrom ChIPSeq Data
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra
- lines changed 166, context: html, text, full: html, text
Added 6 submissions to trackDb
- lines changed 18, context: html, text, full: html, text
Fixed missing subGroup Treatment on tracks
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra
- lines changed 61, context: html, text, full: html, text
Added 2 submissions to Faire-seq track
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.html
- lines changed 19, context: html, text, full: html, text
added 2 new tracks, changed long labels to new model
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.ra
- lines changed 240, context: html, text, full: html, text
added 2 new tracks, changed long labels to new model
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra
- lines changed 23, context: html, text, full: html, text
chnaged long labels to new convention
- lines changed 2, context: html, text, full: html, text
changed long labels, added Tier 1 comment
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.ra
- lines changed 10, context: html, text, full: html, text
changed long labels, added Tier 1 comment
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
- lines changed 336, context: html, text, full: html, text
staging UWDNase on hgwbeta
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra
- lines changed 72, context: html, text, full: html, text
Added 3 submissions to the trackDb and metaDb
- lines changed 94, context: html, text, full: html, text
Fixed some missing data and display issues
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.html
- lines changed 84, context: html, text, full: html, text
Added new track description for Uw TFBS track
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.ra
- lines changed 1084, context: html, text, full: html, text
Added 49 submissions for UW TFBS
- src/hg/makeDb/trackDb/human/hg19/wgEncodeYaleRnaSeq.ra
- src/hg/makeDb/trackDb/human/hgdpGeo.html
- lines changed 19, context: html, text, full: html, text
alphabetized reference list
- src/hg/makeDb/trackDb/human/numtSeq.html
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 7, context: html, text, full: html, text
adding irish snps to genome variants
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Work in progress for Track #683: moving almost all of Belinda'sGenome Variants hgwdev-only subtracks into the main Genome Variants.
Also updating some reference links and adding subtrack matrix settings.
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Added two human Agilent arrays and updated alpha description/trackDb.
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Work in progress for #559: split snp131 into 3 subtracks:Common: uniquely mapped SNPs found by HapMap and/or 1000 Genomes;
Misc: uniquely mapped SNPs;
Non-unique: SNPs that map to more than one genomic location.
Currently I'm only using the validation codes by-hapmap and
by-1000genomes to separate Common and Misc; however, I really
should add a filter on allele frequency because the dbSNP doc
implies that some by-hapmap SNPs only found a single allele,
which would mean they validated that it's not a common SNP.
We don't get allele freq data from dbSNP; would need to fetch
new db dump files etc. It would be great to include allele
freq data in the SNPs track if we go to the trouble, and Jim
has suggested adding a clinically associated bit (although
that bit can be triggered by the most tangential of associations,
like region endpoints in OMIM). Spot-checking other validation
codes, none of them seem reliable enough to use as a basis for
Common. E.g. cluster might be from earlier+later version of same
submitter's bulk submission.
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Oops, lost pgYoruban2 (which will remain hgwdev-only) when merging mypgSnp human/trackDb.ra changes with Belinda's.
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Track #683: Moving the new pgIrish from pgSnpHgwdev to pgSnp.
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Track #1702 (DGV update): add release alpha definition for dataVersion v9 -> v10.
- src/hg/makeDb/trackDb/makefile
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EXTRA should be on all loadTracks commands
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add -p flag to cp of cv.ra (for Brooke)
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remove old copy of cv.ra before cp -p of new one
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remove trix files before making them
- src/hg/makeDb/trackDb/microbat/myoLuc2/description.html
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Initial descriptions for myoLuc2.
- src/hg/makeDb/trackDb/microbat/myoLuc2/gap.html
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Initial descriptions for myoLuc2.
- src/hg/makeDb/trackDb/microbat/myoLuc2/gold.html
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Initial descriptions for myoLuc2.
- src/hg/makeDb/trackDb/microbat/myoLuc2/trackDb.ra
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Initial descriptions for myoLuc2.
- src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
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Added link to euarchontoglire tree model and changed language as per redmine #264 note 18 (copied language from hg19).
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
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Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra
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Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
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Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
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Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
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Turning off vertebrate phyloP by default. (Placental mammal is still on.)
- src/hg/makeDb/trackDb/rat/rn4/rgdGene2.html
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Update for RGD Genes, Redmine issue #29.
- src/hg/makeDb/trackDb/rhesus/refSeqAnno.html
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fixed result of cascading yank and put error (renamed track to drop extra n)
- src/hg/makeDb/trackDb/rhesus/refSeqAnnon.html
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fixed result of cascading yank and put error (renamed track to drop extra n)
- src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
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fixed result of cascading yank and put error (renamed track to drop extra n)
- src/hg/makeDb/trackDb/rhesus/trackDb.ra
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fixed result of cascading yank and put error (renamed track to drop extra n)
- src/hg/makeDb/trackDb/rnaCluster.html
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changed spelling of blat to BLAT
- src/hg/makeDb/trackDb/tagTypes.tab
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Added broadPeak to signalFilter allowed types
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fixed result of cascading yank and put error (renamed track to drop extra n)
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Added support for pennantIcon as requested by b0b. First use flagging hg18 to hg19 liftOver tracks.
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Track #1684 (SNPs 132 (dbSNP)): work in progress: basic tables areloaded (snp132, snp132Exceptions, snp132ExceptionDesc, snp132Seq).
Still need to build ortho alleles, snp132CodingDbSnp; still
need to split up snp132 into subsets which will end up either as
subtracks or individual tracks, TBD; and still need to add new
columns for allele frequency & bitfields (or at least the clinically
assoc'd bit).
- src/hg/makeDb/trackDb/trackDb.ra
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Track #1684 (SNPs 132 (dbSNP)): work in progress: basic tables areloaded (snp132, snp132Exceptions, snp132ExceptionDesc, snp132Seq).
Still need to build ortho alleles, snp132CodingDbSnp; still
need to split up snp132 into subsets which will end up either as
subtracks or individual tracks, TBD; and still need to add new
columns for allele frequency & bitfields (or at least the clinically
assoc'd bit).
- src/hg/makeDb/trackDb/turkey/melGal1/description.html
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Initial descriptions for melGal1.
- src/hg/makeDb/trackDb/turkey/melGal1/gap.html
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Initial descriptions for melGal1.
- src/hg/makeDb/trackDb/turkey/melGal1/gold.html
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Initial descriptions for melGal1.
- src/hg/makeDb/trackDb/turkey/melGal1/trackDb.ra
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Initial descriptions for melGal1.
- src/hg/makeDb/trackDb/wallaby/macEug2/description.html
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Initial descriptions for macEug2.
- src/hg/makeDb/trackDb/wallaby/macEug2/gap.html
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Initial descriptions for macEug2.
- src/hg/makeDb/trackDb/wallaby/macEug2/gold.html
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Initial descriptions for macEug2.
- src/hg/makeDb/trackDb/wallaby/macEug2/trackDb.ra
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Initial descriptions for macEug2.
- src/hg/makeDb/trackDb/worm/bruMal1/description.html
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fixup copy and paste name errors from H. contortus to specific organism
- src/hg/makeDb/trackDb/worm/melHap1/description.html
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fixup copy and paste name errors from H. contortus to specific organism
- src/hg/snp/snpLoad/snpNcbiToUcsc.c
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Tweaks for successfully parsing dbSNP human 132 data.
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Revert "Tweaks for successfully parsing dbSNP human 132 data."
This reverts commit 2deaf8fc3e14d917fda89a30aa15809a7dc4d08e.
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Track #1684 (SNPs 132 (dbSNP)): Tweaks for successfully parsinghuman b132 data.
- src/hg/utils/automation/Encode.pm
- src/hg/utils/gff3ToGenePred/tests/expected/discontinuousTest.gp
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added support for GFF3 discontinuous features
- src/hg/utils/gff3ToGenePred/tests/expected/errCases1Test.out
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added support for GFF3 discontinuous features
- src/hg/utils/gff3ToGenePred/tests/input/discontinuous.gff3
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added support for GFF3 discontinuous features
- src/hg/utils/gff3ToGenePred/tests/makefile
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added support for GFF3 discontinuous features
- src/hg/utils/gff3ToPsl/gff3ToPsl.c
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librarized the cigar to psl code
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renamed cigar converter to make it clear that this is the GFF3 cigar format, not the ENSEMBL cigar
- src/hg/utils/mutationClassifier/mutationClassifier.c
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add geneModel option to accomodate using alternate gene models; use nibTwoCache to read DNA sequences (much faster than using hFetchSeqMixed)
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start adding support for discovery of de novo binding site mutations
- src/hg/visiGene/hgVisiGene/printCaption.c
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using a new field geneId in knownToVisiGene table so that links going back to hgGene will correctly function when there happens to be a panel that has multiple genes/probes including yours but the others mess it up: example nkx2-2 used to take you to Ctnna2
- src/hg/visiGene/knownToVisiGene/knownToVisiGene.c
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adding a new field geneId to knownToVisiGene table so that links going back to hgGene will correctly function when there happens to be a panel that has multiple genes/probes including yours but the others mess it up: example nkx2-2 used to take you to Ctnna2
- src/inc/cheapcgi.h
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Added the color we use widely for sub headers
- src/inc/common.h
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Added a couple of useful macros for boolean settings
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Added some standard bit mask macros
- src/inc/gff3.h
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added support for GFF3 discontinuous features
- src/inc/psl.h
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librarized the cigar to psl code
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renamed cigar converter to make it clear that this is the GFF3 cigar format, not the ENSEMBL cigar
- src/inc/ra.h
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Added raReadWithFilter to read an ra file and collect a set of related stanza. Useful for cv.ra processing to get all antibodies or all cells
- src/lib/basicBed.c
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fixed bug in handling translated psls
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oops do not want commented out code
- src/lib/common.c
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Brian caught me bugging out. case insensitive sort should really be case insensitive
- src/lib/gff3.c
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added support for GFF3 discontinuous features
- src/lib/psl.c
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librarized the cigar to psl code
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renamed cigar converter to make it clear that this is the GFF3 cigar format, not the ENSEMBL cigar
- src/lib/ra.c
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Added raReadWithFilter to read an ra file and collect a set of related stanza. Useful for cv.ra processing to get all antibodies or all cells
- src/lib/tests/expected/gff3DiscontiousTest.out
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added support for GFF3 discontinuous features
- src/lib/tests/expected/gff3ErrorCasesTest.err
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added support for GFF3 discontinuous features
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fixed error case caused by fixing typo in error message
- src/lib/tests/expected/gff3SacCerTest.out
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added support for GFF3 discontinuous features
- src/lib/tests/input/discontinuous.gff3
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added support for GFF3 discontinuous features
- src/lib/tests/makefile
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added support for GFF3 discontinuous features
- src/product/scripts/updateHtml.sh
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it is OK to rsync the js directory now, it is clean
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