CVS changes by file

review to branch (2009-07-15 to 2009-07-21) v211

• src/hg/archaeStuff/scripts/archaeBrowser/AlignmentCompare.pm
  • 1.2 lines changed: 160, context: html, text, full: html, text
    Modified Alignment Compare
• src/hg/archaeStuff/scripts/archaeBrowser/ConservedDomains.pm
  • 1.3 lines changed: 1, context: html, text, full: html, text
    remove hardcode path for rpsblast to use the version in path instead
  • 1.2 lines changed: 54, context: html, text, full: html, text
    Modified Conserved Domains
• src/hg/archaeStuff/scripts/archaeBrowser/Constant.pm
  • 1.34 lines changed: 18, context: html, text, full: html, text
    add Rfam db dir and model dir to set to use the latest data
• src/hg/archaeStuff/scripts/archaeBrowser/GenePrediction.pm
  • 1.7 lines changed: 606, context: html, text, full: html, text
    Adding Gene Prediction
• src/hg/archaeStuff/scripts/archaeBrowser/ncRNA.pm
  • 1.16 lines changed: 2, context: html, text, full: html, text
    add Rfam db dir and model dir to set to use the latest data
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.120 lines changed: 32, context: html, text, full: html, text
    add some new antibodies from wiki: Oct-2 PU.1 Pbx p300
• src/hg/encode/hgEncodeSubmit/app/controllers/pipeline_controller.rb
  • 1.91 lines changed: 5, context: html, text, full: html, text
    resurrecting the progress bar for uploads
  • 1.90 lines changed: 21, context: html, text, full: html, text
    New improved background runner with greater concurrency, throttles on validation and loading, nice-ing of process priorities, fork/exec/zombie-handling, some logging for high server load or high number of processes, some admin functions to display or reset the running-lists
  • 1.89 lines changed: 2, context: html, text, full: html, text
    quick bugfix on an undefined variable access.
• src/hg/encode/hgEncodeSubmit/go.sample
  • 1.5 lines changed: 1, context: html, text, full: html, text
    adding ./ for users without . on path
• src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb
  • 1.16 lines changed: 2, context: html, text, full: html, text
    resurrecting the progress bar for uploads
  • 1.15 lines changed: 31, context: html, text, full: html, text
    New improved background runner with greater concurrency, throttles on validation and loading, nice-ing of process priorities, fork/exec/zombie-handling, some logging for high server load or high number of processes, some admin functions to display or reset the running-lists
• src/hg/encode/hgEncodeSubmit/pipeline_runner.rb
  • 1.3 lines changed: 215, context: html, text, full: html, text
    New improved background runner with greater concurrency, throttles on validation and loading, nice-ing of process priorities, fork/exec/zombie-handling, some logging for high server load or high number of processes, some admin functions to display or reset the running-lists
• src/hg/encode/hgEncodeSubmit/runforever.sample
  • 1.3 lines changed: 1, context: html, text, full: html, text
    typo fix pine to pipe
• src/hg/hgTables/wiggle.c
  • 1.75 lines changed: 8, context: html, text, full: html, text
    In doOutWig, when handling a composite's subtrack table: instead of applying the appropriate subtrack info only to shortLabel and longLabel, keep the whole subtrack tdb. Its type is used below, and we can no longer assume that composite type = subtrack type.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.495 lines changed: 55, context: html, text, full: html, text
    Adding support for Fantom CAGE 4 track and filtering beds based on their name.
• src/hg/hgTracks/bedTrack.c
  • 1.16 lines changed: 3, context: html, text, full: html, text
    Disable next/previous item on bigBed.
• src/hg/hgTracks/chromGraphTrack.c
  • 1.16 lines changed: 4, context: html, text, full: html, text
    imageV2 change to fix position inflation due to portal/dragScrolling
• src/hg/hgTracks/config.c
  • 1.83 lines changed: 6, context: html, text, full: html, text
    narrow special cased AppleWebKit versions in dragZoomingConfig
• src/hg/hgTracks/expRatioTracks.c
  • 1.42 lines changed: 7, context: html, text, full: html, text
    imageV2 change to fix position inflation due to portal/dragScrolling
• src/hg/hgTracks/hgTracks.c
  • 1.1585 lines changed: 1, context: html, text, full: html, text
    Disable next/previous item on bigBed.
• src/hg/hgTracks/imageV2.c
  • 1.6 lines changed: 17, context: html, text, full: html, text
    Limit portal to chromSize. Fix dragScroll in IE which choked on ondrag event.
• src/hg/hgTracks/simpleTracks.c
  • 1.92 lines changed: 1, context: html, text, full: html, text
    bugfix for igtcColor: BayGenomics' suffix is BG.
  • 1.91 lines changed: 7, context: html, text, full: html, text
    imageV2 change to fix position inflation due to portal/dragScrolling
• src/hg/inc/hui.h
  • 1.135 lines changed: 12, context: html, text, full: html, text
    Adding support for Fantom CAGE 4 track and filtering beds based on their name.
• src/hg/inc/trackDb.h
  • 1.51 lines changed: 4, context: html, text, full: html, text
    Adding method for parent to abandon kids
  • 1.50 lines changed: 2, context: html, text, full: html, text
    Adding support for Fantom CAGE 4 track and filtering beds based on their name.
• src/hg/inc/versionInfo.h
  • 1.151 lines changed: 1, context: html, text, full: html, text
    "New version number v211"
• src/hg/js/hgTracks.js
  • 1.31 lines changed: 20, context: html, text, full: html, text
    Limit GET->PUT logic to when page has a form (CEL search creates 500 links and timeouts). Also played with smothing IE dragScroll.
• src/hg/lib/hui.c
  • 1.226 lines changed: 5, context: html, text, full: html, text
    Making composite parent abandon kids without tables before building UI
  • 1.225 lines changed: 1, context: html, text, full: html, text
    Fix bug where default view cfg open was remaining closed
  • 1.224 lines changed: 4, context: html, text, full: html, text
    Handle bed filter ui in multi-view composites
  • 1.223 lines changed: 59, context: html, text, full: html, text
    Adding support for Fantom CAGE 4 track and filtering beds based on their name.
• src/hg/lib/trackDbCustom.c
  • 1.68 lines changed: 24, context: html, text, full: html, text
    Adding method for parent to abandon kids
  • 1.67 lines changed: 3, context: html, text, full: html, text
    Adding support for Fantom CAGE 4 track and filtering beds based on their name.
• src/hg/makeDb/doc/hg18.txt
  • 1.369 lines changed: 26, context: html, text, full: html, text
    Adding some additional documentation
  • 1.368 lines changed: 72, context: html, text, full: html, text
    Adding docs about generating the cage track.
• src/hg/makeDb/doc/makeEnsembl.txt
  • 1.12 lines changed: 948, context: html, text, full: html, text
    Version 55 update done
• src/hg/makeDb/doc/monDom5.txt
  • 1.12 lines changed: 7, context: html, text, full: html, text
    Added note about setting default position.
• src/hg/makeDb/genbank/etc/rr.dbs
  • 1.82 lines changed: 1, context: html, text, full: html, text
    Added monDom5.
• src/hg/makeDb/trackDb/README
  • 1.84 lines changed: 36, context: html, text, full: html, text
    Added some detail about the ClosestToHome paradigm, since this was confusing people
  • 1.83 lines changed: 9, context: html, text, full: html, text
    a few typos
• src/hg/makeDb/trackDb/chimp/panTro1/snp125.html
  • 1.3 lines changed: 14, context: html, text, full: html, text
    added paragraph about the new feature of displaying the function and coding differences relative to particular gene sets.
• src/hg/makeDb/trackDb/cow/bosTau3/snp127.html
  • 1.3 lines changed: 13, context: html, text, full: html, text
    added paragraph about the new feature of displaying the function and coding differences relative to particular gene sets.
• src/hg/makeDb/trackDb/dog/canFam1/snp125.html
  • 1.3 lines changed: 14, context: html, text, full: html, text
    added paragraph about the new feature of displaying the function and coding differences relative to particular gene sets.
• src/hg/makeDb/trackDb/drosophila/bdtnpChipper.html
  • 1.3 lines changed: 4, context: html, text, full: html, text
    fixed up references
• src/hg/makeDb/trackDb/drosophila/trackDb.ra
  • 1.81 lines changed: 4, context: html, text, full: html, text
    shortening some longLabels
  • 1.80 lines changed: 1, context: html, text, full: html, text
    bdtnpChipper settingsByView: fixed other part of sloppy copy/paste (thx Ann).
  • 1.79 lines changed: 1, context: html, text, full: html, text
    fixed typo in configuration of BDTNP track
• src/hg/makeDb/trackDb/genscan.html
  • 1.15 lines changed: 1, context: html, text, full: html, text
    Changed broken link to paper to a DOI link, which should be permanent.
• src/hg/makeDb/trackDb/human/hg18/fantomCageGraphTop.html
  • 1.1 lines changed: 57, context: html, text, full: html, text
    Files for CAGE track
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.404 lines changed: 107, context: html, text, full: html, text
    Adding additional options to trackDb.ra
  • 1.403 lines changed: 53, context: html, text, full: html, text
    Adding support for Fantom CAGE 4 track and filtering beds based on their name.
  • 1.402 lines changed: 9, context: html, text, full: html, text
    removing beta block for snp128 override block. we are hiding snp128 by default now that we have snp130 (so snp130 and snp129 will be on by default)
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.429 lines changed: 2, context: html, text, full: html, text
    The other shoe dropped Gm12878/Pol3 peaks reloaded
  • 1.428 lines changed: 5, context: html, text, full: html, text
    Yale updated 5 sets of peaks
  • 1.427 lines changed: 274, context: html, text, full: html, text
    More UW DNase changes
  • 1.426 lines changed: 74, context: html, text, full: html, text
    Cleaned up some metadata mistakes in Yale
  • 1.425 lines changed: 39, context: html, text, full: html, text
    Affy data for 431
  • 1.424 lines changed: 42, context: html, text, full: html, text
    new data from AFfy
  • 1.423 lines changed: 56, context: html, text, full: html, text
    add some Hudsonalpha control information.
  • 1.422 lines changed: 10, context: html, text, full: html, text
    adding fragsize to labels
  • 1.421 lines changed: 46, context: html, text, full: html, text
    added K562 C12878 cell lines to Hudsonalpha MethylSeq
  • 1.420 lines changed: 3, context: html, text, full: html, text
    Edit label and defaults for consistency
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.html
  • 1.7 lines changed: 8, context: html, text, full: html, text
    add Data Restriction Policy
• src/hg/makeDb/trackDb/human/hg18/wgEncodeNhgriNre.html
  • 1.7 lines changed: 9, context: html, text, full: html, text
    Added Data release policy
  • 1.6 lines changed: 5, context: html, text, full: html, text
    Minor edits
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Minor edits for consistency and clarity
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.37 lines changed: 50, context: html, text, full: html, text
    changed some settings. turned multiz off by default for now
• src/hg/makeDb/trackDb/lamprey/petMar1/description.html
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to genome.wustl.edu.
• src/hg/makeDb/trackDb/lowelab/privateTracks.ra
  • 1.19 lines changed: 6, context: html, text, full: html, text
    add restricted tracks for natrMaga
• src/hg/makeDb/trackDb/lowelab/trackDb.ra
  • 1.78 lines changed: 28, context: html, text, full: html, text
    Adding Gene Prediction Tracks
  • 1.77 lines changed: 13, context: html, text, full: html, text
    add alignInfoAll
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra
  • 1.7 lines changed: 1, context: html, text, full: html, text
    reordered the multiz9way so wallaby is at the top
• src/hg/makeDb/trackDb/phastConsElements.html
  • 1.23 lines changed: 15, context: html, text, full: html, text
    Fixed reference formats.
• src/hg/makeDb/trackDb/rat/rn4/snp125.html
  • 1.2 lines changed: 14, context: html, text, full: html, text
    added paragraph about the new feature of displaying the function and coding differences relative to particular gene sets.
• src/hg/makeDb/trackDb/snp125.html
  • 1.21 lines changed: 13, context: html, text, full: html, text
    added paragraph about the new feature of displaying the function and coding differences relative to particular gene sets.
• src/hg/makeDb/trackDb/snp126.html
  • 1.17 lines changed: 13, context: html, text, full: html, text
    added paragraph about the new feature of displaying the function and coding differences relative to particular gene sets.
• src/hg/makeDb/trackDb/snp127.html
  • 1.3 lines changed: 13, context: html, text, full: html, text
    added paragraph about the new feature of displaying the function and coding differences relative to particular gene sets.
• src/hg/makeDb/trackDb/snp128.html
  • 1.15 lines changed: 13, context: html, text, full: html, text
    added paragraph about the new feature of displaying the function and coding differences relative to particular gene sets.
• src/hg/makeDb/trackDb/snp129.html
  • 1.13 lines changed: 13, context: html, text, full: html, text
    added paragraph about the new feature of displaying the function and coding differences relative to particular gene sets.
• src/hg/makeDb/trackDb/snp130.html
  • 1.9 lines changed: 13, context: html, text, full: html, text
    added paragraph about the new feature of displaying the function and coding differences relative to particular gene sets.
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.521 lines changed: 3, context: html, text, full: html, text
    lower-cased the C in hg19chainNet
• src/hg/makeDb/trackDb/wgEncodeNhgriBip.html
  • 1.5 lines changed: 9, context: html, text, full: html, text
    Added data release policy
• src/hg/makeDb/trackDb/zebrafish/danRer3/rhMap.html
  • 1.9 lines changed: 2, context: html, text, full: html, text
    Removing link to Mark Fishman at Massachusetts General Hospital. There does not seem to be a suitable replacement link.
• src/hg/makeDb/trackDb/zebrafish/danRer4/rhMap.html
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Removing link to Mark Fishman at Massachusetts General Hospital. There does not seem to be a suitable replacement link.
• src/hg/utils/automation/doHgNearBlastp.pl
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Copy-paste error noticed by Brian in code review, thanks!
• src/inc/common.mk
  • 1.64 lines changed: 1, context: html, text, full: html, text
    Adding -g allows ident to work once more. It was optimized out by new C compiler on new hgwdev
  • 1.63 lines changed: 1, context: html, text, full: html, text
    Oops, no space or quote characters in ifeq.
• src/utils/cvsTools/cvscheck
  • 1.1 lines changed: 2, context: html, text, full: html, text
    cvscheck checks for sandbox changes without updating the sandbox
• src/utils/cvsTools/cvsup
  • 1.5 lines changed: 2, context: html, text, full: html, text
    cvscheck checks for sandbox changes without updating the sandbox
  • 1.4 lines changed: 9, context: html, text, full: html, text
    burned once, trying a helping hack
• src/utils/cvsTools/makefile
  • 1.4 lines changed: 1, context: html, text, full: html, text
    cvscheck checks for sandbox changes without updating the sandbox
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.69 lines changed: 3, context: html, text, full: html, text
    v211 final build
• src/utils/qa/weeklybld/coBranch.csh
  • 1.6 lines changed: 6, context: html, text, full: html, text
    handle sandbox configuration
• src/utils/qa/weeklybld/configureSandbox.csh
  • 1.1 lines changed: 48, context: html, text, full: html, text
    make util to help configure a sandbox with settings like SSL,BAM
• src/utils/qa/weeklybld/defaultBuildSettings.mk
  • 1.1 lines changed: 2, context: html, text, full: html, text
    add settings profiles for SSL and BAM
• src/utils/qa/weeklybld/downloadBuildSettings.mk
  • 1.1 lines changed: 2, context: html, text, full: html, text
    add settings profiles for SSL and BAM
• src/utils/qa/weeklybld/makeUserApps.csh
  • 1.3 lines changed: 4, context: html, text, full: html, text
    handle sandbox configuration

• lines changed: 3652
• files changed: 70