All File Changes
v243_preview to v243_preview2 (2010-10-19 to 2010-10-26) v243
- src/ameme/makefile
- lines changed 1, context: html, text, full: html, text
Adding libpng to makefile link line.
- src/hg/checkTableCoords/tests/makefile
- src/hg/encode/DAFs/2.0/psuMm9Tfbs.daf
- lines changed 15, context: html, text, full: html, text
Added 2 new views for replicate signals and peaks
- lines changed 1, context: html, text, full: html, text
Updated required field for veiw
- src/hg/encode/DAFs/2.0/uwChipSeq.daf
- lines changed 1, context: html, text, full: html, text
Fixed typo in dafVersion that existed in these two files
- src/hg/encode/DAFs/2.0/uwTfbs.daf
- lines changed 63, context: html, text, full: html, text
New Daf to support seperation of CTCF and Histone data
- lines changed 4, context: html, text, full: html, text
Updated longlabel Prefixs from Histone to TFBS
- lines changed 1, context: html, text, full: html, text
Fixed typo in dafVersion that existed in these two files
- src/hg/encode/docId/docIdMetaShow/docIdMetaShow.c
- lines changed 71, context: html, text, full: html, text
a CGI to show docId submission pipeline contents
- lines changed 1, context: html, text, full: html, text
marginal improvement. Links into docId directory now. Need to move stuff that calculates path into library and use type metadata rather than funky parsing of filename from metaData
- lines changed 19, context: html, text, full: html, text
closed the loop between the viewer and the submitter
- lines changed 27, context: html, text, full: html, text
moving forward, no submits multiple files, and knows about uncompressed files
- lines changed 3, context: html, text, full: html, text
a little bug with type decoration
- src/hg/encode/docId/docIdMetaShow/makefile
- lines changed 17, context: html, text, full: html, text
a CGI to show docId submission pipeline contents
- src/hg/encode/docId/docIdSubmitDir/docIdSubmitDir.c
- lines changed 90, context: html, text, full: html, text
marginal improvement. Links into docId directory now. Need to move stuff that calculates path into library and use type metadata rather than funky parsing of filename from metaData
- lines changed 104, context: html, text, full: html, text
closed the loop between the viewer and the submitter
- lines changed 65, context: html, text, full: html, text
moving forward, no submits multiple files, and knows about uncompressed files
- src/hg/encode/docId/docIdSubmitDir/makefile
- lines changed 1, context: html, text, full: html, text
closed the loop between the viewer and the submitter
- src/hg/encode/docId/inc/docId.h
- lines changed 7, context: html, text, full: html, text
closed the loop between the viewer and the submitter
- lines changed 2, context: html, text, full: html, text
moving forward, no submits multiple files, and knows about uncompressed files
- src/hg/encode/docId/lib/docIdSub.c
- lines changed 99, context: html, text, full: html, text
closed the loop between the viewer and the submitter
- lines changed 16, context: html, text, full: html, text
moving forward, no submits multiple files, and knows about uncompressed files
- lines changed 2, context: html, text, full: html, text
a little bug with type decoration
- src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
- lines changed 1, context: html, text, full: html, text
keeping tableName and fileIndex off the downloads page
- src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
- lines changed 10, context: html, text, full: html, text
added better errors for missing one-row-table look ups
- src/hg/encode/encodeValidate/config/cv.ra
- lines changed 28, context: html, text, full: html, text
Registered 2 antibodies and validation documents for Myers lab
- lines changed 4, context: html, text, full: html, text
Registered an appropriate protcol document for the combined registration of GM12878 XiMat and XiPat cell lines, with clones
- lines changed 5, context: html, text, full: html, text
Added Yale_TFBS(Struhl) growth protocol registration
- lines changed 1, context: html, text, full: html, text
Added a new A549 cell protocol
- lines changed 1, context: html, text, full: html, text
Renamed a hyperlink for a protocol file
- lines changed 31, context: html, text, full: html, text
Registered to new antibodies c-Myc and Mxi-1 for Snyder lab
- lines changed 5, context: html, text, full: html, text
Registered new EtOH treatment for the Snyder lab
- src/hg/encode/hgEncodeSubmit/app/controllers/pipeline_controller.rb
- lines changed 273, context: html, text, full: html, text
mass-ftp submissions is working
- lines changed 91, context: html, text, full: html, text
added support for mass submissions from url list
- src/hg/encode/hgEncodeSubmit/app/views/layouts/main.rhtml
- lines changed 2, context: html, text, full: html, text
mass-ftp submissions is working
- src/hg/encode/hgEncodeSubmit/app/views/pipeline/mass_ftp.rhtml
- lines changed 50, context: html, text, full: html, text
mass-ftp submissions is working
- lines changed 2, context: html, text, full: html, text
added support for mass submissions from url list
- src/hg/encode/hgEncodeSubmit/app/views/pipeline/mass_tools.rhtml
- lines changed 15, context: html, text, full: html, text
mass-ftp submissions is working
- src/hg/encode/hgEncodeSubmit/app/views/pipeline/mass_url.rhtml
- lines changed 58, context: html, text, full: html, text
mass-ftp submissions is working
- lines changed 45, context: html, text, full: html, text
added support for mass submissions from url list
- src/hg/encode/hgEncodeSubmit/app/views/pipeline/show_tools.rhtml
- lines changed 10, context: html, text, full: html, text
mass-ftp submissions is working
- src/hg/encode/hgEncodeSubmit/app/views/pipeline/upload.rhtml
- lines changed 1, context: html, text, full: html, text
added support for mass submissions from url list
- src/hg/hgBlat/hgBlat.c
- lines changed 43, context: html, text, full: html, text
Redmine Feature #1470 (create ability to not have a blat server for anassembly):
1. In hgBlat, if db does not have a blat server, search for an
alternate as hgPcr does: if there's a blat server for the same
organism, use that, otherwise just default to the db with a blat
server & the lowest dbDb.orderKey. If we default to some other
db's blat server, notify the user.
2. In hgPcr, if we default to some other db's blat server, notify the user.
3. If db doesn't have a blat server, suppress the blat links in the
hot links bar in webStartWrapperDetailedInternal. (hgTracks.c's hot
links already did this). Our static html hotlinks include Blat and
PCR links, so it is still necessary for hgBlat and hgPcr to handle
db's that don't have blat servers.
4. Also in webStartWrapperDetailedInternal, call getDbAndGenome (part
of uiState construction) *before* we test db for NULL and default
the local db variable to hDefaultDb. When the defaulting happened
before getDbAndGenome (as in hgVisiGene which passes in NULL db),
db was hDefaultDb for a while and then the cart db, and the hot
links weren't constructed correctly.
- src/hg/hgGateway/hgGateway.c
- lines changed 19, context: html, text, full: html, text
Fixed loss of assembly when choosing this before track search. Simplified messy multi-form design
- lines changed 8, context: html, text, full: html, text
Mostly refiguring to ensure shorter 'get' URL. Paging will remember previous selections but may remove this code.
- lines changed 12, context: html, text, full: html, text
Fixed extra lines in FF and different extra lines in IE. Changed bgcolor of copyright notice to no longer differ from rest. Other than that, changed as little as possible.
- lines changed 1, context: html, text, full: html, text
Made bg image of blue guidelines a reusable file so browsers can cache it. Made trackSearch dependent upon advanced javascript features.
- src/hg/hgKnownGeneList/hgKnownGeneList.c
- lines changed 6, context: html, text, full: html, text
Cleaned up some comments and code as suggested by Jim
- src/hg/hgPcr/hgPcr.c
- lines changed 6, context: html, text, full: html, text
Redmine Feature #1470 (create ability to not have a blat server for anassembly):
1. In hgBlat, if db does not have a blat server, search for an
alternate as hgPcr does: if there's a blat server for the same
organism, use that, otherwise just default to the db with a blat
server & the lowest dbDb.orderKey. If we default to some other
db's blat server, notify the user.
2. In hgPcr, if we default to some other db's blat server, notify the user.
3. If db doesn't have a blat server, suppress the blat links in the
hot links bar in webStartWrapperDetailedInternal. (hgTracks.c's hot
links already did this). Our static html hotlinks include Blat and
PCR links, so it is still necessary for hgBlat and hgPcr to handle
db's that don't have blat servers.
4. Also in webStartWrapperDetailedInternal, call getDbAndGenome (part
of uiState construction) *before* we test db for NULL and default
the local db variable to hDefaultDb. When the defaulting happened
before getDbAndGenome (as in hgVisiGene which passes in NULL db),
db was hDefaultDb for a while and then the cart db, and the hot
links weren't constructed correctly.
- src/hg/hgTables/gffOut.c
- lines changed 5, context: html, text, full: html, text
Code Review #1452 (v243 preview1): Melissa pointed out that cdsSizewas incorrectly computed when there is a single coding exon that
contains both 5' and 3' UTR plus the entire coding region. Fixed.
This didn't cause symptoms because in that single-coding-exon case,
there is no next coding exon so the miscalculated value is unused.
- lines changed 5, context: html, text, full: html, text
Code Review #1452 (v243 preview1): Melissa pointed out that makingoffsetToGenomic recursive would be more robust than assuming that
the answer must lie either in this exon or the next one.
- src/hg/hgTracks/cds.c
- lines changed 104, context: html, text, full: html, text
Redmine Feature #953 (mRNA non-synonomous codons don't work whengenome is a stop):
In cds.c, genomic stop codons were encoded into grayIx as 'X' which
unfortunately is also an error return from dnautil.c's lookupCodon.
Genomic 'X' codons (including stop codons) were excluded from
detection of non-synonymous codons -- thus the invisibility of
difference when genome has a stop codon but mRNAs don't. Since 'X'
can be caused by something valid like an N in the codon, I don't think
it makes sense to exclude it from comparison. Also, I changed the
grayIx encoding to use 'J' for stop codon (not a valid peptide code
and not X). Also did some refactoring to abstract out the grayIx
encoding a bit, and make names a bit more accurate.
- src/hg/hgTracks/config.c
- lines changed 14, context: html, text, full: html, text
Mostly refiguring to ensure shorter 'get' URL. Paging will remember previous selections but may remove this code.
- lines changed 34, context: html, text, full: html, text
move advancedJavascriptFeaturesEnabled to jsHelper.c
- lines changed 1, context: html, text, full: html, text
Made bg image of blue guidelines a reusable file so browsers can cache it. Made trackSearch dependent upon advanced javascript features.
- src/hg/hgTracks/hgTracks.c
- lines changed 1, context: html, text, full: html, text
Fixed number 20 from Katrina's list. Blue bar hotlink form hgTrackUi to 'Genome Browser' had returned to searchTracks if came from there.
- lines changed 3, context: html, text, full: html, text
add a advancedJavascriptFeaturesEnabled check
- lines changed 17, context: html, text, full: html, text
Mostly refiguring to ensure shorter 'get' URL. Paging will remember previous selections but may remove this code.
- lines changed 32, context: html, text, full: html, text
Made bg image of blue guidelines a reusable file so browsers can cache it. Made trackSearch dependent upon advanced javascript features.
- src/hg/hgTracks/hgTracks.h
- lines changed 3, context: html, text, full: html, text
move advancedJavascriptFeaturesEnabled to jsHelper.c
- lines changed 1, context: html, text, full: html, text
Needed to make sure all of hgTracks can access jsHelper::advancedJavacriptFeatures()
- src/hg/hgTracks/imageV2.c
- lines changed 3, context: html, text, full: html, text
default configureByPopup to off for snp, conservation and multiz tracks
- lines changed 1, context: html, text, full: html, text
Parent label needed encoding in json. Fixed 1071-26
- src/hg/hgTracks/mainMain.c
- lines changed 2, context: html, text, full: html, text
Mostly refiguring to ensure shorter 'get' URL. Paging will remember previous selections but may remove this code.
- src/hg/hgTracks/searchTracks.c
- lines changed 2, context: html, text, full: html, text
Fixed number 18 on Katrina's list. Supertrack childen were showing as visibile when their parent was hide
- lines changed 1, context: html, text, full: html, text
Fixed number 20 from Katrina's list. Blue bar hotlink form hgTrackUi to 'Genome Browser' had returned to searchTracks if came from there.
- lines changed 393, context: html, text, full: html, text
Chopped up doSearchTracks into some logical subroutines. Nothing changed except spacing of 'About' section at bottom of page.
- lines changed 144, context: html, text, full: html, text
Search buttons back into tab div and changed some font sizes
- lines changed 3, context: html, text, full: html, text
ignore metaDb cart settings if metaDb doesn't exist (fixed issues 24 in ticket 1071)
- lines changed 13, context: html, text, full: html, text
remove metaDbExists parameter from printMdbSelects call
- lines changed 19, context: html, text, full: html, text
handle invalid metaDb values when switching assemblies
- lines changed 77, context: html, text, full: html, text
Mostly refiguring to ensure shorter 'get' URL. Paging will remember previous selections but may remove this code.
- lines changed 5, context: html, text, full: html, text
Made bg image of blue guidelines a reusable file so browsers can cache it. Made trackSearch dependent upon advanced javascript features.
- src/hg/htdocs/goldenPath/help/trackSearch.html
- lines changed 1, context: html, text, full: html, text
add info about ENCODE terms not being in every assembly's track search
- lines changed 15, context: html, text, full: html, text
making Mary's edits suggested in Issue #936 (note 18)
- src/hg/inc/jsHelper.h
- lines changed 3, context: html, text, full: html, text
move advancedJavascriptFeaturesEnabled to jsHelper.c
- src/hg/inc/mdb.h
- lines changed 2, context: html, text, full: html, text
make qsort callback public
- lines changed 4, context: html, text, full: html, text
Cleaned up some comments and code as suggested by Jim
- lines changed 3, context: html, text, full: html, text
add a new function that returns and mdbVar given a var name
- src/hg/inc/searchTracks.h
- lines changed 7, context: html, text, full: html, text
Mostly refiguring to ensure shorter 'get' URL. Paging will remember previous selections but may remove this code.
- lines changed 3, context: html, text, full: html, text
Made bg image of blue guidelines a reusable file so browsers can cache it. Made trackSearch dependent upon advanced javascript features.
- src/hg/inc/trashDir.h
- lines changed 4, context: html, text, full: html, text
Added tracksDirReusableFile so that hgTracks bg image of blue lines can be reused.
- src/hg/inc/web.h
- lines changed 6, context: html, text, full: html, text
Cleaned up some comments and code as suggested by Jim
- src/hg/js/ajax.js
- lines changed 10, context: html, text, full: html, text
refactor code into removeHgsid
- src/hg/js/hgTracks.js
- lines changed 6, context: html, text, full: html, text
refactor code into removeHgsid
- lines changed 10, context: html, text, full: html, text
Restrict track description popup to 900px and set focus on search input in some restricted cases.
- lines changed 5, context: html, text, full: html, text
ignore configureByPopup setting for description only popups and add target='_blank' to links
- lines changed 33, context: html, text, full: html, text
Mostly refiguring to ensure shorter 'get' URL. Paging will remember previous selections but may remove this code.
- src/hg/js/utils.js
- lines changed 4, context: html, text, full: html, text
fix getAllVars to handle radio buttons
- src/hg/lib/genes_rat.sql
- lines changed 46, context: html, text, full: html, text
Checking in .sql for RGD Genes build. Issue #29.
- src/hg/lib/hdb.c
- lines changed 1, context: html, text, full: html, text
hIsBlatIndexedDatabase was looking in dbDb instead of blatServers, oops. Fixed.
- src/hg/lib/jsHelper.c
- lines changed 34, context: html, text, full: html, text
move advancedJavascriptFeaturesEnabled to jsHelper.c
- src/hg/lib/mdb.c
- lines changed 11, context: html, text, full: html, text
Cleaned up some comments and code as suggested by Jim
- lines changed 13, context: html, text, full: html, text
add a new function that returns and mdbVar given a var name
- src/hg/lib/rgdGene2KeggPathway.sql
- lines changed 9, context: html, text, full: html, text
Created rgdGene2KeggPathway.sql for RGD Genes build, issue #29.
- src/hg/lib/rgdGene2Pep.sql
- lines changed 7, context: html, text, full: html, text
Checking in .sql for RGD Genes build. Issue #29.
- src/hg/lib/rgdGene2ToDescription.sql
- lines changed 7, context: html, text, full: html, text
Checking in .sql for RGD Genes build. Issue #29.
- src/hg/lib/rgdGene2ToDisplayId.sql
- lines changed 8, context: html, text, full: html, text
Checking in .sql for RGD Genes build. Issue #29.
- src/hg/lib/rgdGene2ToKeggEntrez.sql
- lines changed 7, context: html, text, full: html, text
Checking in .sql for RGD Genes build. Issue #29.
- src/hg/lib/rgdGene2ToPDB.sql
- lines changed 8, context: html, text, full: html, text
Checking in .sql for RGD Genes build. Issue #29.
- src/hg/lib/rgdGene2ToSuper.sql
- lines changed 8, context: html, text, full: html, text
Checking in .sql for RGD Genes build. Issue #29.
- src/hg/lib/rgdGene2ToSymbol.sql
- lines changed 10, context: html, text, full: html, text
Checking in .sql for RGD Genes build. Issue #29.
- src/hg/lib/rgdGene2ToUniProt.sql
- lines changed 8, context: html, text, full: html, text
Checking in .sql for RGD Genes build. Issue #29.
- src/hg/lib/searchTracks.c
- lines changed 4, context: html, text, full: html, text
add config variable to put trix file somewhere else
- lines changed 6, context: html, text, full: html, text
Made bg image of blue guidelines a reusable file so browsers can cache it. Made trackSearch dependent upon advanced javascript features.
- src/hg/lib/trashDir.c
- lines changed 21, context: html, text, full: html, text
Added tracksDirReusableFile so that hgTracks bg image of blue lines can be reused.
- src/hg/lib/web.c
- lines changed 3, context: html, text, full: html, text
Fixed number 20 from Katrina's list. Blue bar hotlink form hgTrackUi to 'Genome Browser' had returned to searchTracks if came from there.
- lines changed 14, context: html, text, full: html, text
Cleaned up some comments and code as suggested by Jim
- lines changed 7, context: html, text, full: html, text
Mostly refiguring to ensure shorter 'get' URL. Paging will remember previous selections but may remove this code.
- lines changed 2, context: html, text, full: html, text
add ability to put styleDir and styleImagesDir in hg.conf
- lines changed 42, context: html, text, full: html, text
Redmine Feature #1470 (create ability to not have a blat server for anassembly):
1. In hgBlat, if db does not have a blat server, search for an
alternate as hgPcr does: if there's a blat server for the same
organism, use that, otherwise just default to the db with a blat
server & the lowest dbDb.orderKey. If we default to some other
db's blat server, notify the user.
2. In hgPcr, if we default to some other db's blat server, notify the user.
3. If db doesn't have a blat server, suppress the blat links in the
hot links bar in webStartWrapperDetailedInternal. (hgTracks.c's hot
links already did this). Our static html hotlinks include Blat and
PCR links, so it is still necessary for hgBlat and hgPcr to handle
db's that don't have blat servers.
4. Also in webStartWrapperDetailedInternal, call getDbAndGenome (part
of uiState construction) *before* we test db for NULL and default
the local db variable to hDefaultDb. When the defaulting happened
before getDbAndGenome (as in hgVisiGene which passes in NULL db),
db was hDefaultDb for a while and then the cart db, and the hot
links weren't constructed correctly.
- src/hg/makeDb/doc/bruMal1.txt
- lines changed 33, context: html, text, full: html, text
finishing up melHap1 and bruMal1
- src/hg/makeDb/doc/caeJap3.txt
- lines changed 23, context: html, text, full: html, text
wrapping up ce9,cb3,caeJap3,caePb2,priPac2 with default tracks and visibilities and all.joiner definitions
- lines changed 34, context: html, text, full: html, text
caejap3 in pushQ and default tracks for caeJap3 and priPac2
- src/hg/makeDb/doc/cb3.txt
- lines changed 48, context: html, text, full: html, text
wrapping up ce9,cb3,caeJap3,caePb2,priPac2 with default tracks and visibilities and all.joiner definitions
- src/hg/makeDb/doc/ce9.txt
- lines changed 11, context: html, text, full: html, text
wrapping up ce9,cb3,caeJap3,caePb2,priPac2 with default tracks and visibilities and all.joiner definitions
- src/hg/makeDb/doc/encodeDccHg18/broadBernstein.txt
- lines changed 747, context: html, text, full: html, text
Finally moved make encode make docs from hg18 to hg19 for hg19 submissions. Thus most of this check in is nothing new. However, broadHistone has been updated this week with submissions
- src/hg/makeDb/doc/encodeDccHg18/dukeUtaUncCrawford.txt
- lines changed 967, context: html, text, full: html, text
Finally moved make encode make docs from hg18 to hg19 for hg19 submissions. Thus most of this check in is nothing new. However, broadHistone has been updated this week with submissions
- src/hg/makeDb/doc/encodeDccHg18/haibChipSeq.txt
- lines changed 474, context: html, text, full: html, text
Finally moved make encode make docs from hg18 to hg19 for hg19 submissions. Thus most of this check in is nothing new. However, broadHistone has been updated this week with submissions
- src/hg/makeDb/doc/encodeDccHg18/uwStam.txt
- lines changed 570, context: html, text, full: html, text
Finally moved make encode make docs from hg18 to hg19 for hg19 submissions. Thus most of this check in is nothing new. However, broadHistone has been updated this week with submissions
- src/hg/makeDb/doc/encodeDccHg18/yaleDavisHarvardSnyder.txt
- lines changed 214, context: html, text, full: html, text
Finally moved make encode make docs from hg18 to hg19 for hg19 submissions. Thus most of this check in is nothing new. However, broadHistone has been updated this week with submissions
- src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt
- lines changed 1477, context: html, text, full: html, text
Finally moved make encode make docs from hg18 to hg19 for hg19 submissions. Thus most of this check in is nothing new. However, broadHistone has been updated this week with submissions
- src/hg/makeDb/doc/encodeDccHg19/haibTfbsMyers.hg19.txt
- lines changed 476, context: html, text, full: html, text
Finally moved make encode make docs from hg18 to hg19 for hg19 submissions. Thus most of this check in is nothing new. However, broadHistone has been updated this week with submissions
- src/hg/makeDb/doc/encodeDccHg19/openChromCrawford.hg19.txt
- lines changed 969, context: html, text, full: html, text
Finally moved make encode make docs from hg18 to hg19 for hg19 submissions. Thus most of this check in is nothing new. However, broadHistone has been updated this week with submissions
- src/hg/makeDb/doc/encodeDccHg19/sydnSnyder.hg19.txt
- lines changed 216, context: html, text, full: html, text
Finally moved make encode make docs from hg18 to hg19 for hg19 submissions. Thus most of this check in is nothing new. However, broadHistone has been updated this week with submissions
- src/hg/makeDb/doc/encodeDccHg19/uwStam.hg19.txt
- lines changed 572, context: html, text, full: html, text
Finally moved make encode make docs from hg18 to hg19 for hg19 submissions. Thus most of this check in is nothing new. However, broadHistone has been updated this week with submissions
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlShort.release1.notes
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwAffyExonArray.release1.notes
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwDgf.release1.notes
- lines changed 195, context: html, text, full: html, text
Added the release notes for Release 1 of UW DGF track
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwDnase.release1.notes
- lines changed 1085, context: html, text, full: html, text
Added Change note fore Release 1 of Uw Dnase track
- lines changed 12, context: html, text, full: html, text
Added 4 files that were missing
- src/hg/makeDb/doc/haeCon1.txt
- lines changed 31, context: html, text, full: html, text
done with haeCon1 default tracks and assembly documentation
- src/hg/makeDb/doc/hg19.txt
- src/hg/makeDb/doc/melHap1.txt
- lines changed 30, context: html, text, full: html, text
finishing up melHap1 and bruMal1
- src/hg/makeDb/doc/melInc1.txt
- lines changed 30, context: html, text, full: html, text
done with melInc1 default tracks and documentation and in the pushQ
- src/hg/makeDb/doc/priPac2.txt
- lines changed 79, context: html, text, full: html, text
wrapping up ce9,cb3,caeJap3,caePb2,priPac2 with default tracks and visibilities and all.joiner definitions
- lines changed 15, context: html, text, full: html, text
caejap3 in pushQ and default tracks for caeJap3 and priPac2
- src/hg/makeDb/doc/proteins/090821.txt
- lines changed 58, context: html, text, full: html, text
Created rgdGene2KeggPathway.sql for RGD Genes build, issue #29.
- src/hg/makeDb/genbank/etc/align.dbs
- src/hg/makeDb/genbank/etc/genbank.conf
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- src/hg/makeDb/hgFakeAgp/makefile
- src/hg/makeDb/schema/all.joiner
- lines changed 12, context: html, text, full: html, text
wrapping up ce9,cb3,caeJap3,caePb2,priPac2 with default tracks and visibilities and all.joiner definitions
- lines changed 4, context: html, text, full: html, text
done with haeCon1 default tracks and assembly documentation
- lines changed 4, context: html, text, full: html, text
done with melInc1 default tracks and documentation and in the pushQ
- lines changed 5, context: html, text, full: html, text
finishing up melHap1 and bruMal1
- src/hg/makeDb/schema/joinerCheck/joinerCheck.c
- lines changed 13, context: html, text, full: html, text
verify specified database is legitimate
- src/hg/makeDb/trackDb/README
- lines changed 4, context: html, text, full: html, text
default configureByPopup to off for snp, conservation and multiz tracks
- src/hg/makeDb/trackDb/cat/felCat4/gold.html
- lines changed 2, context: html, text, full: html, text
removing references to N and U sequences which don't apply to this assembly
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 20, context: html, text, full: html, text
fixed Katrinas request for CSHL Long not having filename in the metadata
- src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
- lines changed 6, context: html, text, full: html, text
removed the metadata project line bug #1301
- lines changed 20, context: html, text, full: html, text
fixed Katrinas request for CSHL Long not having filename in the metadata
- src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncodeYaleRnaSeq.ra
- lines changed 6, context: html, text, full: html, text
removed the metadata project line bug #1301
- src/hg/makeDb/trackDb/human/hg18/wgEncodeBuOrchid.ra
- lines changed 6, context: html, text, full: html, text
removed the metadata project line bug #1301
- src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.ra
- lines changed 80, context: html, text, full: html, text
removed the metadata project line bug #1301
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaRnaSeq.ra
- lines changed 12, context: html, text, full: html, text
removed the metadata project line bug #1301
- src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.ra
- lines changed 57, context: html, text, full: html, text
removed the metadata project line bug #1301
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
- lines changed 3, context: html, text, full: html, text
adding YaleRnaSeq to the list of files to go in metaDB
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
- lines changed 1409, context: html, text, full: html, text
Broad's fastqs for experiments new to hg19
- lines changed 2509, context: html, text, full: html, text
Imported metadata from hg18 for fastq files that have not changed
- lines changed 17, context: html, text, full: html, text
Corrections to the last set
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 17, context: html, text, full: html, text
fixed dates for origAssembly
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
- lines changed 321, context: html, text, full: html, text
new data with orgi assembly and dates
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
- lines changed 649, context: html, text, full: html, text
Added meta-data for 9 submissions from Open Chrom group
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
- lines changed 485, context: html, text, full: html, text
Added meta-data for 9 submissions from Open Chrom group
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
- lines changed 199, context: html, text, full: html, text
changed dates to reflect resubmit
- lines changed 5, context: html, text, full: html, text
collection of changes after approval call
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeYaleRnaSeq.ra
- lines changed 106, context: html, text, full: html, text
changed the wgEncodeYale track all the way around
- lines changed 15, context: html, text, full: html, text
adding YaleRnaSeq to the list of files to go in metaDB
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
- lines changed 1, context: html, text, full: html, text
staging metaDb for affyRnaLoc on beta
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeAffyRnaChip.ra
- lines changed 1977, context: html, text, full: html, text
staging metaDb for affyRnaLoc on beta
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.html
- lines changed 6, context: html, text, full: html, text
fixed typos and clarified some of the references
- lines changed 2, context: html, text, full: html, text
clarified Transfrags references
- src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.html
- lines changed 1, context: html, text, full: html, text
added information about the pink-purple color
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.ra
- lines changed 44, context: html, text, full: html, text
changed short labels to match kate
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra
- lines changed 25, context: html, text, full: html, text
Set track short and long labels for hg19 standard, based on Jim's input
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.html
- lines changed 4, context: html, text, full: html, text
Updated sentence in Track Description
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra
- lines changed 142, context: html, text, full: html, text
Added 5 submissions to track
- lines changed 12, context: html, text, full: html, text
Fixed typos in trackDb treatments
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra
- lines changed 109, context: html, text, full: html, text
Added 4 submissions to track
- lines changed 12, context: html, text, full: html, text
Fixed typos in trackDb treatments
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.ra
- lines changed 27, context: html, text, full: html, text
final on/off adjustments for tracks
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.html
- lines changed 7, context: html, text, full: html, text
collection of changes after approval call
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.ra
- lines changed 126, context: html, text, full: html, text
removed rep 3, changed order of matrix
- lines changed 115, context: html, text, full: html, text
collection of changes after approval call
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.html
- lines changed 30, context: html, text, full: html, text
Updated release notes about bad bams
- src/hg/makeDb/trackDb/human/hg19/wgEncodeYaleRnaSeq.html
- lines changed 120, context: html, text, full: html, text
changed the wgEncodeYale track all the way around
- src/hg/makeDb/trackDb/human/hg19/wgEncodeYaleRnaSeq.ra
- lines changed 116, context: html, text, full: html, text
changed the wgEncodeYale track all the way around
- src/hg/makeDb/trackDb/human/omimGene.html
- lines changed 2, context: html, text, full: html, text
made disclaimer all bold to match decipher
- src/hg/makeDb/trackDb/trackDb.chainNet.ra
- lines changed 112, context: html, text, full: html, text
wrapping up ce9,cb3,caeJap3,caePb2,priPac2 with default tracks and visibilities and all.joiner definitions
- src/hg/makeDb/trackDb/worm/caeJap3/description.html
- lines changed 70, context: html, text, full: html, text
wrapping up ce9,cb3,caeJap3,caePb2,priPac2 with default tracks and visibilities and all.joiner definitions
- src/hg/makeDb/trackDb/worm/caeJap3/gap.html
- lines changed 63, context: html, text, full: html, text
wrapping up ce9,cb3,caeJap3,caePb2,priPac2 with default tracks and visibilities and all.joiner definitions
- src/hg/makeDb/trackDb/worm/caeJap3/gold.html
- lines changed 25, context: html, text, full: html, text
wrapping up ce9,cb3,caeJap3,caePb2,priPac2 with default tracks and visibilities and all.joiner definitions
- src/hg/makeDb/trackDb/worm/caeJap3/trackDb.ra
- lines changed 41, context: html, text, full: html, text
caejap3 in pushQ and default tracks for caeJap3 and priPac2
- src/hg/makeDb/trackDb/worm/caePb2/trackDb.ra
- lines changed 3, context: html, text, full: html, text
wrapping up ce9,cb3,caeJap3,caePb2,priPac2 with default tracks and visibilities and all.joiner definitions
- src/hg/makeDb/trackDb/worm/cb3/trackDb.ra
- lines changed 17, context: html, text, full: html, text
wrapping up ce9,cb3,caeJap3,caePb2,priPac2 with default tracks and visibilities and all.joiner definitions
- src/hg/makeDb/trackDb/worm/ce9/description.html
- lines changed 106, context: html, text, full: html, text
up to date documentation pages
- src/hg/makeDb/trackDb/worm/ce9/gap.html
- lines changed 70, context: html, text, full: html, text
up to date documentation pages
- src/hg/makeDb/trackDb/worm/ce9/gold.html
- lines changed 29, context: html, text, full: html, text
up to date documentation pages
- src/hg/makeDb/trackDb/worm/ce9/trackDb.ra
- lines changed 17, context: html, text, full: html, text
setting default visibilities
- src/hg/makeDb/trackDb/worm/haeCon1/description.html
- lines changed 40, context: html, text, full: html, text
done with haeCon1 default tracks and assembly documentation
- src/hg/makeDb/trackDb/worm/haeCon1/gap.html
- lines changed 60, context: html, text, full: html, text
done with haeCon1 default tracks and assembly documentation
- src/hg/makeDb/trackDb/worm/haeCon1/gold.html
- lines changed 25, context: html, text, full: html, text
done with haeCon1 default tracks and assembly documentation
- src/hg/makeDb/trackDb/worm/haeCon1/trackDb.ra
- lines changed 41, context: html, text, full: html, text
done with haeCon1 default tracks and assembly documentation
- src/hg/makeDb/trackDb/worm/melHap1/description.html
- lines changed 4, context: html, text, full: html, text
finishing up melHap1 and bruMal1
- src/hg/makeDb/trackDb/worm/melHap1/gap.html
- lines changed 63, context: html, text, full: html, text
finishing up melHap1 and bruMal1
- src/hg/makeDb/trackDb/worm/melHap1/gold.html
- lines changed 19, context: html, text, full: html, text
finishing up melHap1 and bruMal1
- src/hg/makeDb/trackDb/worm/melInc1/gap.html
- lines changed 63, context: html, text, full: html, text
done with melInc1 default tracks and documentation and in the pushQ
- src/hg/makeDb/trackDb/worm/melInc1/gold.html
- lines changed 19, context: html, text, full: html, text
done with melInc1 default tracks and documentation and in the pushQ
- src/hg/makeDb/trackDb/worm/melInc1/trackDb.ra
- lines changed 48, context: html, text, full: html, text
done with melInc1 default tracks and documentation and in the pushQ
- src/hg/makeDb/trackDb/worm/priPac2/description.html
- lines changed 55, context: html, text, full: html, text
wrapping up ce9,cb3,caeJap3,caePb2,priPac2 with default tracks and visibilities and all.joiner definitions
- src/hg/makeDb/trackDb/worm/priPac2/gap.html
- lines changed 61, context: html, text, full: html, text
wrapping up ce9,cb3,caeJap3,caePb2,priPac2 with default tracks and visibilities and all.joiner definitions
- src/hg/makeDb/trackDb/worm/priPac2/gold.html
- lines changed 34, context: html, text, full: html, text
wrapping up ce9,cb3,caeJap3,caePb2,priPac2 with default tracks and visibilities and all.joiner definitions
- lines changed 1, context: html, text, full: html, text
done with haeCon1 default tracks and assembly documentation
- src/hg/makeDb/trackDb/worm/priPac2/trackDb.ra
- lines changed 19, context: html, text, full: html, text
wrapping up ce9,cb3,caeJap3,caePb2,priPac2 with default tracks and visibilities and all.joiner definitions
- lines changed 44, context: html, text, full: html, text
caejap3 in pushQ and default tracks for caeJap3 and priPac2
- src/hg/makeDb/trackDb/worm/trackDb.chainNet.ra
- src/hg/makeDb/trackDb/worm/trackDb.ra
- lines changed 56, context: html, text, full: html, text
wrapping up ce9,cb3,caeJap3,caePb2,priPac2 with default tracks and visibilities and all.joiner definitions
- src/hg/makeDb/trackDb/worm/ws210Gene.html
- lines changed 13, context: html, text, full: html, text
catching up ce9 tracks on the nematodes
- src/hg/utils/automation/makeDownloads.pl
- lines changed 1, context: html, text, full: html, text
done with haeCon1 default tracks and assembly documentation
- src/hg/utils/automation/makePushQSql.pl
- lines changed 5, context: html, text, full: html, text
done with haeCon1 default tracks and assembly documentation
- lines changed 8, context: html, text, full: html, text
up to date genbank table listing
- src/hg/utils/makeTrackIndex/makeTrackIndex.c
- lines changed 1, context: html, text, full: html, text
add short label (per jim kent)
- src/hg/utils/phyloTrees/ce9.10way.dissect.txt
- lines changed 133, context: html, text, full: html, text
tree diagrams for 10-way nematodes
- src/hg/utils/phyloTrees/ce9.10way.nh
- lines changed 3, context: html, text, full: html, text
tree diagrams for 10-way nematodes
- src/hg/utils/phyloTrees/ce9.chainNet.pl
- lines changed 120, context: html, text, full: html, text
tree diagrams for 10-way nematodes
- src/lib/trix.c
- lines changed 2, context: html, text, full: html, text
fix problem in findOrderedSpan; it was returning span - 1 in cases where an item had a span with all words and then some, but not all, of the words after the span (this caused problem in track search)
- src/product/README.install
- lines changed 20, context: html, text, full: html, text
add note about locking down the trash directory
- src/product/README.trackDb
- lines changed 4, context: html, text, full: html, text
add note about wiki page and the other options to avoid extFile confusion
- src/product/ex.hg.conf
- lines changed 6, context: html, text, full: html, text
add some conf variables that support using something other than the default style files
- lines changed 4, context: html, text, full: html, text
added a way to specify the path to get the trix file from trackSearch
- src/tracks/makefile
- lines changed 1, context: html, text, full: html, text
Adding libpng to makefile link line.
- src/utils/qa/graph.csh
- lines changed 1, context: html, text, full: html, text
added comment abt default width to usage statement
- src/utils/qa/weeklybld/buildEnv.csh
- src/weblet/counter/makefile
- lines changed 1, context: html, text, full: html, text
Adding libpng to makefile link line.
- lines changed: 22382
- files changed: 247