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
  • lines changed 2, context: html, text, full: html, text
    fixup stderr reroute
• 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 60, context: html, text, full: html, text
    pretty up a little
  • 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 1, context: html, text, full: html, text
    increase buf size
  • 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.
  • lines changed 18, context: html, text, full: html, text
    More twiddling with css
• 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 this again.
  • 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.
  • lines changed 3, context: html, text, full: html, text
    More twiddling with css
• 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
  • lines changed 16, context: html, text, full: html, text
    added fastqs
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwAffyExonArray.release1.notes
  • lines changed 268, context: html, text, full: html, text
    new notes file
• 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
  • lines changed 32, context: html, text, full: html, text
    GENE BOUNDS done
• 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 35, context: html, text, full: html, text
    priPac2 in the pushQ
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    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
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    adding priPac2
• src/hg/makeDb/genbank/etc/genbank.conf
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    Added priPac2.
• src/hg/makeDb/genbank/etc/hgwdev.dbs
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    adding priPac2
• src/hg/makeDb/hgFakeAgp/makefile
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    do not need jkap lib
• src/hg/makeDb/schema/all.joiner
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    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
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    done with melInc1 default tracks and documentation and in the pushQ
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    finishing up melHap1 and bruMal1
• src/hg/makeDb/schema/joinerCheck/joinerCheck.c
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    verify specified database is legitimate
• src/hg/makeDb/trackDb/README
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    default configureByPopup to off for snp, conservation and multiz tracks
• src/hg/makeDb/trackDb/cat/felCat4/gold.html
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    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
  • lines changed 210, context: html, text, full: html, text
    added fastqs
• 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
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    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
  • lines changed 1, context: html, text, full: html, text
    YaleRnaSeq added
• 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
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    clarified Transfrags references
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.ra
  • lines changed 104, context: html, text, full: html, text
    removed metadata lines
• 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
  • lines changed 1, context: html, text, full: html, text
    turned off color mode
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
  • lines changed 165, context: html, text, full: html, text
    Sig to Signal
• 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
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    label changes
• 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
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    up to date documentation pages
• src/hg/makeDb/trackDb/worm/ce9/gap.html
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    up to date documentation pages
• src/hg/makeDb/trackDb/worm/ce9/gold.html
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    up to date documentation pages
• src/hg/makeDb/trackDb/worm/ce9/trackDb.ra
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    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
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    done with haeCon1 default tracks and assembly documentation
• src/hg/makeDb/trackDb/worm/haeCon1/gold.html
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    done with haeCon1 default tracks and assembly documentation
• src/hg/makeDb/trackDb/worm/haeCon1/trackDb.ra
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    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
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    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
  • lines changed 48, context: html, text, full: html, text
    adding ce7ChainNet
• 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
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    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
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    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
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    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
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    added comment abt default width to usage statement
• src/utils/qa/weeklybld/buildEnv.csh
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    v243 preview2
• src/weblet/counter/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding libpng to makefile link line.

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• files changed: 247