All File Changes

v278_preview2 to v278_base (2013-01-15 to 2013-01-22) v278

• src/hg/hgGateway/hgGateway.c
  • lines changed 2, context: html, text, full: html, text
    added support for database-based GUI menu items in Mirror menu. also added support for hg.conf browser.geoSuffix for testing. got rid of unneeded javascript in globalNav.inc and put C code instead into geoMirror.c
• src/hg/hgSession/hgSession.c
  • lines changed 2, context: html, text, full: html, text
    Set the udc cache dir correctly because otherwise when a saved session that has bigDataUrl custom tracks gets loaded it will incorrectly use the path /tmp/udcCache/, however the path it should use is in hg.conf and calling setUdcCacheDir() will read and use that setting udc.cacheDir=../trash/udcCache
• src/hg/hgTracks/menu.c
  • lines changed 1, context: html, text, full: html, text
    added support for database-based GUI menu items in Mirror menu. also added support for hg.conf browser.geoSuffix for testing. got rid of unneeded javascript in globalNav.inc and put C code instead into geoMirror.c
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    #9269 qPCR Primers code improved based on Angie's CR #9966 feedback.
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    added line for papAnu2
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 3, context: html, text, full: html, text
    added credits for papAnu2
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 2, context: html, text, full: html, text
    modified sentence, see redmine #9999
  • lines changed 1, context: html, text, full: html, text
    made a minor correction, see redmine #9999 note-7
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 31, context: html, text, full: html, text
    Added new item about petMar2 release (redmine #9153)
  • lines changed 25, context: html, text, full: html, text
    added announcement for baboon assembly papAnu2
  • lines changed 1, context: html, text, full: html, text
    corrected announcement date for papAnu2
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 67, context: html, text, full: html, text
    added support for database-based GUI menu items in Mirror menu. also added support for hg.conf browser.geoSuffix for testing. got rid of unneeded javascript in globalNav.inc and put C code instead into geoMirror.c
• src/hg/htdocs/indexNews.html
  • lines changed 58, context: html, text, full: html, text
    Added new item about petMar2 release (redmine #9153)
  • lines changed 158, context: html, text, full: html, text
    added announcement for new baboon assembly papAnu2
• src/hg/inc/geoMirror.h
  • lines changed 6, context: html, text, full: html, text
    added support for database-based GUI menu items in Mirror menu. also added support for hg.conf browser.geoSuffix for testing. got rid of unneeded javascript in globalNav.inc and put C code instead into geoMirror.c
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v278
• src/hg/lib/geoMirror.c
  • lines changed 72, context: html, text, full: html, text
    added support for database-based GUI menu items in Mirror menu. also added support for hg.conf browser.geoSuffix for testing. got rid of unneeded javascript in globalNav.inc and put C code instead into geoMirror.c
• src/hg/lib/trackDbCustom.c
  • lines changed 3, context: html, text, full: html, text
    Add ENCODE track types to packable list. They've generally been used in track hierarchies where packability appeared as a side-effect.
• src/hg/lib/web.c
  • lines changed 22, context: html, text, full: html, text
    added support for database-based GUI menu items in Mirror menu. also added support for hg.conf browser.geoSuffix for testing. got rid of unneeded javascript in globalNav.inc and put C code instead into geoMirror.c
• src/hg/makeDb/doc/encodeDccHg19/awgUniform.txt
  • lines changed 2, context: html, text, full: html, text
    Adding step for linking md5sum files properly in downloads. Response to QA. #9850 ENCODE Uniform DNaseI HS
• src/hg/makeDb/doc/hg19.txt
  • lines changed 69, context: html, text, full: html, text
    added affyCytoScan track
  • lines changed 2, context: html, text, full: html, text
    #9269 qPCR Primers code improved based on Angie's CR #9966 feedback.
• src/hg/makeDb/doc/mm10.txt
  • lines changed 2, context: html, text, full: html, text
    #9269 qPCR Primers code improved based on Angie's CR #9966 feedback.
• src/hg/makeDb/doc/papAnu2.txt
  • lines changed 14, context: html, text, full: html, text
    Track #9965 liftOver to/from papHam1 <-> papAnu2
• src/hg/makeDb/doc/papHam1.txt
  • lines changed 15, context: html, text, full: html, text
    Track #9965 liftOver to/from papHam1 <-> papAnu2
• src/hg/makeDb/doc/susScr2.txt
  • lines changed 12, context: html, text, full: html, text
    readmine #8533 NumtS track for susScr2 continue...
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    added papAnu2 assembly
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    added papAnu2 assembly
• src/hg/makeDb/genbank/src/copy/gbMakeDownload
  • lines changed 4, context: html, text, full: html, text
    build downloads for xenoRefGene #9991
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    added affyCytoScan to tablesIgnored
  • lines changed 1, context: html, text, full: html, text
    Added coriellDelDup to hg19 tablesIgnored (redmine #6530)
  • lines changed 5, context: html, text, full: html, text
    add rules for the mm10Strains1 superTrack
• src/hg/makeDb/trackDb/baboon/papAnu2/description.html
  • lines changed 1, context: html, text, full: html, text
    Added sentence about species change, see redmine #8166 note-10
• src/hg/makeDb/trackDb/baboon/papHam1/description.html
  • lines changed 1, context: html, text, full: html, text
    added sentence about species change, see redmine #8166 note-10
• src/hg/makeDb/trackDb/chainNet.html
  • lines changed 2, context: html, text, full: html, text
    Changing back reference links to point to articles, Code Review #9973
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 1, context: html, text, full: html, text
    Allow comma separated list for DCC Accession. Added so that integrative analysis tracks that merge experiments can include the underlying experiments (without a lot of additional development for nested experiments or whatever). Used in #9850 ENCODE Uniform DNaseI HS.
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 68, context: html, text, full: html, text
    Copying alpha/cv.ra to beta/cv.ra
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 68, context: html, text, full: html, text
    Copying beta/cv.ra to public/cv.ra, in part preparation of ENCODE AWG Uniform DNase (Release 1) RM#9850 -new AWG cv.ra term
• src/hg/makeDb/trackDb/drosophila/bdtnpChipper.html
  • lines changed 32, context: html, text, full: html, text
    Updated References section
• src/hg/makeDb/trackDb/drosophila/bdtnpChipperOld.html
  • lines changed 32, context: html, text, full: html, text
    Updated References section
• src/hg/makeDb/trackDb/drosophila/bdtnpDnase.html
  • lines changed 22, context: html, text, full: html, text
    Updated References section
• src/hg/makeDb/trackDb/human/affyTxnPhase2.html
  • lines changed 16, context: html, text, full: html, text
    Updated References section; edited reference to Chuck Sugnet; made other minor corrections (redmine #7554)
• src/hg/makeDb/trackDb/human/altSeqComposite.html
  • lines changed 2, context: html, text, full: html, text
    Changing back reference links to point to articles, Code Review #9973
• src/hg/makeDb/trackDb/human/hg19/chainSelf.html
  • lines changed 2, context: html, text, full: html, text
    Changing back reference links to point to articles, Code Review #9973
• src/hg/makeDb/trackDb/human/hg19/genotypeArrays.html
  • lines changed 7, context: html, text, full: html, text
    added comment about colors in affyCytoScan array
• src/hg/makeDb/trackDb/human/hg19/haibTfbs.txt
  • lines changed 1755, context: html, text, full: html, text
    Fixing merge conflict
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/.nfs000000001c22961e000002bd
  • lines changed 43, context: html, text, full: html, text
    Fixing merge conflict
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/acc.csh
  • lines changed 43, context: html, text, full: html, text
    Fixing merge conflict
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/acc.out
  • lines changed 2, context: html, text, full: html, text
    Fixing merge conflict
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/new.txt
  • lines changed 127, context: html, text, full: html, text
    Fixing merge conflict
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/test.csh
  • lines changed 6, context: html, text, full: html, text
    Fixing merge conflict
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgDnaseUniform.ra
  • lines changed 15, context: html, text, full: html, text
    Add dccAccessions to metadata for merged experiments. #9850 ENCODE Uniform DNaseI HS
  • lines changed 1, context: html, text, full: html, text
    Filling in missing second accession for UW+Duke Th1 dataset, but need to double-check this with AWG as the cell registration for this is not the same (Adult_CD4+_Th1, Th1)
  • lines changed 1, context: html, text, full: html, text
    Updating mdb magic number
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeAwgDnaseUniform.ra
  • lines changed 16, context: html, text, full: html, text
    Staging metaData to beta for AWG Uniform DNase (Release 1) RM#9850
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    Staging metaData to public for ENCODE AWG DNase (Release 1) RM#9850
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeAwgDnaseUniform.ra
  • lines changed 1881, context: html, text, full: html, text
    Staging metaData to public for ENCODE AWG DNase (Release 1) RM#9850
• src/hg/makeDb/trackDb/human/hg19/tfbsRanges.txt
  • lines changed 1404, context: html, text, full: html, text
    Fixing merge conflict
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    added search for affyCytoScan probesets
  • lines changed 9, context: html, text, full: html, text
    made affyCytoScan search case-insensitive
  • lines changed 8, context: html, text, full: html, text
    removing block for Andy's version of affyCytoScan. was checked in by accident, I think
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Staging metaData to public for ENCODE AWG DNase (Release 1) RM#9850
• src/hg/makeDb/trackDb/human/hg19/viewLimits.txt
  • lines changed 44, context: html, text, full: html, text
    Fixing merge conflict
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.html
  • lines changed 41, context: html, text, full: html, text
    Adding whitespaces and non-html-friendly quotes, small html edits for AWG DNase Uniform Release 1 RM#9850
  • lines changed 1, context: html, text, full: html, text
    Small edit to remove introduced repeat of the word track for AWG DNase Uniform (Release1) RM#9850
  • lines changed 6, context: html, text, full: html, text
    Making links relative for AWG DNase Uniform (Release1) RM#9850
  • lines changed 15, context: html, text, full: html, text
    Add explanation of Tier 2* designation in subtrack list. Response to QA. #9850: ENCODE Uniform DNaseI HS
  • lines changed 20, context: html, text, full: html, text
    Fixing merge conflict
  • lines changed 1, context: html, text, full: html, text
    removing ; from line in AWG Uniform DNase (Release 1)
  • lines changed 7, context: html, text, full: html, text
    Advise on use of UCSC accession listed in metadata and File UI. #9850 ENCODE Uniform DNaseI HS
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.ra
  • lines changed 128, context: html, text, full: html, text
    Able to remove subtrack types and add narrowPeak at composite level if canPack setting is used to work-around incorrect visibility options problem. #9850 ENCODE Uniform DNaseI HS
  • lines changed 7, context: html, text, full: html, text
    Restoring corrections lost in a previous reversion (short label length, signalFilter settings, Huh7.5 tablename
  • lines changed 5, context: html, text, full: html, text
    Fix cell line coloring, in response to QA (Question 7). #9850 ENCODE Uniform DNaseI HS
  • lines changed 3, context: html, text, full: html, text
    Tweak gray scale shading settings to better distinguish differing signal values which are not well distributed. #9850 ENCODE Uniform DNaseI HS
  • lines changed 27, context: html, text, full: html, text
    Friendlier formatting of long subgroup.
  • lines changed 2, context: html, text, full: html, text
    Removing treatment column from fileUi -- it's not very informative and doesn't sort well. The treatment is viewable in the Additional Details. Subject to veto by AQA... #9850 ENCODE Uniform DNaseI HS
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 8, context: html, text, full: html, text
    Added GENCODE V14 to the Release Notes section (redmine #9804)
  • lines changed 1, context: html, text, full: html, text
    Changed version/date of corresponding Ensembl version per http://www.gencodegenes.org/releases/ (redmine #9804)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV14.html
  • lines changed 4, context: html, text, full: html, text
    Since ENCODE metadata is no longer used, removed the line about clicking the down arrow to see metadata; made other minor corrections (redmine #9804)
  • lines changed 1, context: html, text, full: html, text
    Changed version/date of corresponding Ensembl version per http://www.gencodegenes.org/releases/ (redmine #9804)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV14.ra
  • lines changed 42, context: html, text, full: html, text
    fixed search on pseudogenes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegDnaseClustered.release2.html
  • lines changed 2, context: html, text, full: html, text
    Track description wordsmithing
• src/hg/makeDb/trackDb/human/iscaComposite.html
  • lines changed 25, context: html, text, full: html, text
    Made some minor corrections (redmine #9289)
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 25, context: html, text, full: html, text
    Removed release tags for Affy Txn Phase 2 items (redmine #7554)
  • lines changed 7, context: html, text, full: html, text
    added search for coriell track
• src/hg/makeDb/trackDb/mouse/mm10/knownGene.html
  • lines changed 202, context: html, text, full: html, text
    updated mm10 description page
  • lines changed 39, context: html, text, full: html, text
    fixed make error
  • lines changed 1, context: html, text, full: html, text
    changed hg19 to mm10
• src/hg/makeDb/trackDb/mouse/mm10/mm10Strains1.html
  • lines changed 98, context: html, text, full: html, text
    alternate strain track becomes a superTrack according to note 8 requests in redmine 7341
  • lines changed 3, context: html, text, full: html, text
    do not need a reference to hgdownload since all items lead to genbank sequence download
  • lines changed 4, context: html, text, full: html, text
    Made minor corrections (redmine #7341)
• src/hg/makeDb/trackDb/mouse/mm10/mm10Strains1SuperTrack.ra
  • lines changed 38, context: html, text, full: html, text
    alternate strain track becomes a superTrack according to note 8 requests in redmine 7341
  • lines changed 1, context: html, text, full: html, text
    default vis dense for the PSL display
  • lines changed 1, context: html, text, full: html, text
    plenty of room for the Alternate strains shortLabel
  • lines changed 1, context: html, text, full: html, text
    lose the lift over mention, make the longLable read what it really means, redmine 7341
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    alternate strain track becomes a superTrack according to note 8 requests in redmine 7341
  • lines changed 1, context: html, text, full: html, text
    redmine 9269: Move qPCR Primers tracl to 'Expression' group for hg19, for mm10, move to 'Expression and Requlation' grouip.
• src/hg/makeDb/trackDb/qPcrPrimers.html
  • lines changed 45, context: html, text, full: html, text
    Changed wording in several places for readability and to match our conventions, removed reference to specific human/mouse builds, added link to UCSC Genes track description, changed references to fit CBSE citation format. RM #9269.
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    Several changes from conversation with data contributer (RM 9269#note-64). Added better explanation of naming system. Moved link to batch query site to display conventions section. Split step 7 of Description section into two parts, so they could be easily referenced.
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    Wording changes to naming section.
• src/hg/makeDb/trackDb/rhino/cerSim1/description.html
  • lines changed 2, context: html, text, full: html, text
    Updated NCBI assembly link (redmine #8752)
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    Using scoreMax in #9850 ENCODE Uniform DNaseI HS, so adding to narrowPeak list. scoreMin already had this
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    redmine 9269: Move qPCR Primers tracl to 'Expression' group for hg19, for mm10, move to 'Expression and Requlation' grouip.
  • lines changed 1, context: html, text, full: html, text
    #9269 qPCR Primers code improved based on Angie's CR #9966 feedback.
• src/oneShot/wordsBySize/makefile
  • lines changed 18, context: html, text, full: html, text
    Example program to use for job hunters.
• src/oneShot/wordsBySize/wordsBySize.c
  • lines changed 295, context: html, text, full: html, text
    Example program to use for job hunters.
  • lines changed 2, context: html, text, full: html, text
    Improving comments.
  • lines changed 8, context: html, text, full: html, text
    Improved some comments.
  • lines changed 2, context: html, text, full: html, text
    Restored buffer size (was testing error handling and forgot to set it back)
  • lines changed 1, context: html, text, full: html, text
    Improved some comments.
• src/utils/qa/backupCentral.csh
  • lines changed 1, context: html, text, full: html, text
    Removed references gdbPdb, as this table is no longer in use (RM #9803.)
• src/utils/qa/checkMetaData.csh
  • lines changed 10, context: html, text, full: html, text
    Removed references gdbPdb, as this table is no longer in use (RM #9803.)
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v278 final build

• lines changed: 7407
• files changed: 113