All File Changes

v236_preview to v236_base (2010-07-13 to 2010-07-20) v236

• src/hg/das/tests/makefile
  • lines changed 6, context: html, text, full: html, text
    added test case from Sanger bug report
• src/hg/encode/encodeValidate/config/cv.ra
  • lines changed 240, context: html, text, full: html, text
    Adding the new caltech-RNA seq tracks and fixing cv.ra to comment out ripTgtProtiens until we are ready
  • lines changed 2, context: html, text, full: html, text
    NH-A is no longer provisional
  • lines changed 23, context: html, text, full: html, text
    Changed all references to Yale_TFSB to Yale_TFBS
  • lines changed 92, context: html, text, full: html, text
    Added 1 submission 1623 to SYDH TFBS Track
  • lines changed 19, context: html, text, full: html, text
    Added growth protocol to protocols
  • lines changed 15, context: html, text, full: html, text
    Provisionally added NH-A to finish Broad's pre-AWG meeting submissions
• src/hg/encode/encodeValidate/config/expVars.ra
  • lines changed 3, context: html, text, full: html, text
    added wgEncodeYaleRNAseq exp vars
• src/hg/encode/encodeValidate/test/input/chipseq/StanfordChip-Test-Jun08.DDF
  • lines changed 5, context: html, text, full: html, text
    Added 1 submission 1623 to SYDH TFBS Track
• src/hg/encode/encodeValidate/test/input/chipseq/StanfordChip.DAF
  • lines changed 11, context: html, text, full: html, text
    Added 1 submission 1623 to SYDH TFBS Track
• src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb
  • lines changed 29, context: html, text, full: html, text
    increased expansion timeout by a factor of 10 and added better reporting of timeouts
• src/hg/encode/hgEncodeSubmit/pipeline_runner.rb
  • lines changed 1, context: html, text, full: html, text
    making sure that jobs waiting longest get first chance to run
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 2, context: html, text, full: html, text
    Added 1 submission 1623 to SYDH TFBS Track
• src/hg/hgGateway/hgGateway.c
  • lines changed 7, context: html, text, full: html, text
    fix spacing in find tracks
  • lines changed 3, context: html, text, full: html, text
    add find tracks button
• src/hg/hgTracks/config.c
  • lines changed 6, context: html, text, full: html, text
    add find tracks button
• src/hg/hgTracks/factorSource.c
  • lines changed 4, context: html, text, full: html, text
    check for existence of wgEncodeRegTfbsClusteredMotifs
  • lines changed 25, context: html, text, full: html, text
    look for high-confidence motifs in wgEncodeRegTfbsClusteredMotifs
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    add #include searchTracks.h
  • lines changed 13, context: html, text, full: html, text
    move find tracks to the left and only shown when functionality is supported for this db
  • lines changed 2, context: html, text, full: html, text
    Left a </TD> in Mark's Dink buttons
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    move TRACK_SEARCH #define to inc/searchTracks.h
  • lines changed 1, context: html, text, full: html, text
    oops; I checked in previous copy with TRACK_SEARCH turned on
  • lines changed 3, context: html, text, full: html, text
    move #define searchTracks to searchTracks.h
• src/hg/hgTracks/imageV2.c
  • lines changed 23, context: html, text, full: html, text
    Fix obscure bug where apostophe in title was interpreted as close quote - thus screwing up html interpretation
• src/hg/hgTracks/mainMain.c
  • lines changed 1, context: html, text, full: html, text
    add #include searchTracks.h
• src/hg/hgTracks/makefile
  • lines changed 8, context: html, text, full: html, text
    add comment about install of hgRenderTracks
• src/hg/hgTracks/searchTracks.c
  • lines changed 5, context: html, text, full: html, text
    modify temporary comments list
  • lines changed 6, context: html, text, full: html, text
    refactor some code into lib/searchTracks.c and some code-review changes
  • lines changed 15, context: html, text, full: html, text
    ui tweaking
• src/hg/hgc/hgc.c
  • lines changed 4, context: html, text, full: html, text
    Refined DECIPHER detailed page.
• src/hg/hgc/hgc.h
  • lines changed 3, context: html, text, full: html, text
    add motifMultipleHitsSection
• src/hg/hgc/regMotif.c
  • lines changed 23, context: html, text, full: html, text
    add motifMultipleHitsSection
• src/hg/htdocs/ENCODE/cellTypesMouse.html
  • lines changed 1, context: html, text, full: html, text
    changed URL from hard-coded to relative link
  • lines changed 42, context: html, text, full: html, text
    modifying page to reflect Mouse cell types (no tiers), add link to controlled vocab, link to strain info
• src/hg/htdocs/ENCODE/index.html
  • lines changed 36, context: html, text, full: html, text
    split ENCODE portal leftbar into 3 sections & added links to ENCODE Mouse pages, Session Gallery, Registered Variables & Data Standards
• src/hg/htdocs/ENCODE/otherTerms.html
  • lines changed 64, context: html, text, full: html, text
    changed title, moved links to other cv pages to top, added mouse strains, lessened right margin, increased height of some frames
• src/hg/htdocs/ENCODE/releaseLog.html
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 3, context: html, text, full: html, text
    "Encode release log update"
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 17, context: html, text, full: html, text
    adding conservation track for danRer6 to the front page as a small bit (that's why edited newsarch too)
• src/hg/htdocs/goldenPath/releaseLog.html
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 15, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 3, context: html, text, full: html, text
    "Release log update"
• src/hg/htdocs/indexNews.html
  • lines changed 18, context: html, text, full: html, text
    adding conservation track for danRer6 to the front page as a small bit (that's why edited newsarch too)
• src/hg/htdocs/makefile
  • lines changed 5, context: html, text, full: html, text
    don't do git update except on beta install
• src/hg/inc/searchTracks.h
  • lines changed 3, context: html, text, full: html, text
    move TRACK_SEARCH #define to inc/searchTracks.h
  • lines changed 2, context: html, text, full: html, text
    add #define searchTracks
  • lines changed 16, context: html, text, full: html, text
    searchTracks routines which are shared b/n CGIs
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    "New version number v236"
• src/hg/js/hgTracks.js
  • lines changed 8, context: html, text, full: html, text
    changeSearchVisibilityPopups
• src/hg/js/utils.js
  • lines changed 122, context: html, text, full: html, text
    Added beginning of common poupBox and working embedBox for ajax retreived cfg dialogs.
• src/hg/lib/hui.c
  • lines changed 30, context: html, text, full: html, text
    Fixed dimZ bug that Jim noticed. Also cleand up <B><EM></B></EM> failed nesting
• src/hg/lib/knownCanonToDecipher.sql
  • lines changed 6, context: html, text, full: html, text
    Refined DECIPHER detailed page.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    add searchTracks.o
• src/hg/lib/mdb.c
  • lines changed 83, context: html, text, full: html, text
    Fix table name lookup so that it isn't too smart by half
• src/hg/lib/searchTracks.c
  • lines changed 4, context: html, text, full: html, text
    move TRACK_SEARCH #define to inc/searchTracks.h
  • lines changed 19, context: html, text, full: html, text
    searchTracks routines which are shared b/n CGIs
• src/hg/makeDb/doc/bosTau4.txt
  • lines changed 15, context: html, text, full: html, text
    bosTau4 to bosTau5 liftOver
• src/hg/makeDb/doc/bosTau5.txt
  • lines changed 762, context: html, text, full: html, text
    Initial setup for bosTau5.
• src/hg/makeDb/doc/calJac3.txt
  • lines changed 141, context: html, text, full: html, text
    adding quality track
• src/hg/makeDb/doc/hg18.txt
  • lines changed 18, context: html, text, full: html, text
    Refined DECIPHER detailed page.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 3, context: html, text, full: html, text
    Refined hgIkmc processing to deal with some troublesome records.
• src/hg/makeDb/doc/mm9.txt
  • lines changed 24, context: html, text, full: html, text
    working on phyloP for 30way
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    adding felCat4 to beta genBank ups
• src/hg/makeDb/hgLoadMaf/makefile
  • lines changed 4, context: html, text, full: html, text
    get rid of hgLoadMafSummary during cgi build
• src/hg/makeDb/trackDb/checkMetaDb
  • lines changed 1, context: html, text, full: html, text
    add -f option to rm command for metaDb file
  • lines changed 1, context: html, text, full: html, text
    rm metaDb file
• src/hg/makeDb/trackDb/cow/bosTau5/description.html
  • lines changed 129, context: html, text, full: html, text
    Initial descriptions for bosTau5.
• src/hg/makeDb/trackDb/cow/bosTau5/gap.html
  • lines changed 64, context: html, text, full: html, text
    Initial descriptions for bosTau5.
• src/hg/makeDb/trackDb/cow/bosTau5/gold.html
  • lines changed 23, context: html, text, full: html, text
    Initial descriptions for bosTau5.
• src/hg/makeDb/trackDb/cow/bosTau5/trackDb.ra
  • lines changed 40, context: html, text, full: html, text
    Initial descriptions for bosTau5.
• src/hg/makeDb/trackDb/human/darned.html
  • lines changed 8, context: html, text, full: html, text
    more darned changes requested by sponsor
  • lines changed 15, context: html, text, full: html, text
    updating DARNED rna editing trackDb.ra and descr html as requested by sponsor
• src/hg/makeDb/trackDb/human/decipher.html
  • lines changed 13, context: html, text, full: html, text
    Remove upper case of the warning message.
  • lines changed 15, context: html, text, full: html, text
    Made the warning message to UPPER case.
  • lines changed 6, context: html, text, full: html, text
    aesthetic changes to decipher description
  • lines changed 19, context: html, text, full: html, text
    Refined DECIPHER detailed page.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 40, context: html, text, full: html, text
    change tags to release alpha,beta for regulation track
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    Chagning dimZ to dimA to avoid bug in 3-state code
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    add wgEncodeGisDnaPet
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 240, context: html, text, full: html, text
    Oops. These new things should be marked 'post' freeze
  • lines changed 1614, context: html, text, full: html, text
    Metadata update for resubmitted BAMs and 2 more cell lines
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 1329, context: html, text, full: html, text
    add new tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra
  • lines changed 103, context: html, text, full: html, text
    add wgEncodeGisDnaPet
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
  • lines changed 577, context: html, text, full: html, text
    add new datasets to HaibMethylSeq
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 135, context: html, text, full: html, text
    Added 1 submission 1623 to SYDH TFBS Track
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    add gisDnaPet
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeCaltechRnaSeq.ra
  • lines changed 196, context: html, text, full: html, text
    Adding the new caltech-RNA seq tracks and fixing cv.ra to comment out ripTgtProtiens until we are ready
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeSydhTfbs.ra
  • lines changed 23, context: html, text, full: html, text
    Added 1 submission 1623 to SYDH TFBS Track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.ra
  • lines changed 181, context: html, text, full: html, text
    Added 2 more cell lines for Broad
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.ra
  • lines changed 24, context: html, text, full: html, text
    add gisDnaPet
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra
  • lines changed 112, context: html, text, full: html, text
    add new datasets to HaibMethylSeq
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra
  • lines changed 417, context: html, text, full: html, text
    Updated UW Histone, labels and display to be more standardized across supertrack and ENCODE tracks
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    more darned changes requested by sponsor
  • lines changed 2, context: html, text, full: html, text
    updating DARNED rna editing trackDb.ra and descr html as requested by sponsor
• src/hg/makeDb/trackDb/makeMetaDb
  • lines changed 1, context: html, text, full: html, text
    rm metaDb file
  • lines changed 1, context: html, text, full: html, text
    rm metaDb file after building metaDb
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    Added bosTau5 to DBS.
• src/hg/makeDb/trackDb/marmoset/calJac3/bacEnds.html
  • lines changed 36, context: html, text, full: html, text
    adding marmoset bac ends
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    add search spec for bacEndSingles
  • lines changed 1, context: html, text, full: html, text
    adding marmoset bac ends
• src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
  • lines changed 566, context: html, text, full: html, text
    initial content from existing multiz30way html and hg19 cons46way html
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 525, context: html, text, full: html, text
    Added 1 submission for Stanford/Yale Mouse Histone. Also updated all metaData and short and long labels
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 2650, context: html, text, full: html, text
    Added 10 new Mouse Stan/Yale TFBS Submissions. Fixed metadata for update bam files
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 190, context: html, text, full: html, text
    adding phyloP tracks to cons30way composite
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 30, context: html, text, full: html, text
    Added 1 submission for Stanford/Yale Mouse Histone. Also updated all metaData and short and long labels
  • lines changed 214, context: html, text, full: html, text
    Added 10 new Mouse Stan/Yale TFBS Submissions. Fixed metadata for update bam files
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 19, context: html, text, full: html, text
    adding quality track as a bigWig
• src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html
  • lines changed 37, context: html, text, full: html, text
    removing references to conserved elements, tidying up spacing and other general edits
• src/hg/near/hgNear/hgNearData/kegg.html
  • lines changed 2, context: html, text, full: html, text
    Reworded slightly.
• src/hg/ratStuff/mafSplit/makefile
  • lines changed 1, context: html, text, full: html, text
    fixup bare use of make instead use MAKE
• src/hg/utils/automation/Encode.pm
  • lines changed 4, context: html, text, full: html, text
    Non-ideal special case code to force replicate to 1 when no replicate entered for pooled data
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 1, context: html, text, full: html, text
    stray ce9 left in where db should be, code review wins
• src/hg/utils/motifFinder/motifFinder.c
  • lines changed 40, context: html, text, full: html, text
    default to markov0 for background
  • lines changed 25, context: html, text, full: html, text
    pick hight scoring hit within sets of overlapping hits
• src/hg/utils/mutationClassifier/mutationClassifier.c
  • lines changed 10, context: html, text, full: html, text
    default to mark0 for background
• src/inc/dnaMotif.h
  • lines changed 3, context: html, text, full: html, text
    add dnaMotifBitScoreWithMark0Bg
• src/lib/cheapcgi.c
  • lines changed 7, context: html, text, full: html, text
    change cgiMakeDropListClassWithStyleAndJavascript to tolerate all permuations of NULL for parameters
• src/lib/dnaMotif.c
  • lines changed 21, context: html, text, full: html, text
    add dnaMotifBitScoreWithMark0Bg
• src/lib/valgrind.suppress
  • lines changed 3, context: html, text, full: html, text
    update suppressions due to code changes
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v236 final build
• src/utils/qa/weeklybld/buildHgCentralSql.csh
  • lines changed 1, context: html, text, full: html, text
    fixing path for hgcentral.sql push

• lines changed: 11811
• files changed: 131