All File Changes

v239_preview to v239_base (2010-08-24 to 2010-08-31) v239

• src/hg/encode/DAFs/2.0/rikenCageSolexa.daf
  • lines changed 5, context: html, text, full: html, text
    updating with what we actually have been using
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 9, context: html, text, full: html, text
    optimize download zipping with pigz and gzip archive direct appending
  • lines changed 2, context: html, text, full: html, text
    fix using pigz with installed-from-rpm path
• src/hg/encode/encodeValidate/config/cv.ra
  • lines changed 90, context: html, text, full: html, text
    This cv.ra has lab with projectName, note I think that matching tags is going to break this, and I did not spearate into grant and lab because Broad would break it as Broad is both a grant and a lab and in the cv, it can not be both
  • lines changed 22, context: html, text, full: html, text
    Added RNA extract terms for Yale
  • lines changed 4, context: html, text, full: html, text
    Added valdiation document and antibody order url for YY1
  • lines changed 885, context: html, text, full: html, text
    The ripAntibody table is no more
• src/hg/encode/encodeValidate/config/fields.ra
  • lines changed 25, context: html, text, full: html, text
    comments from Kate and Tim
  • lines changed 3, context: html, text, full: html, text
    replaced input with control to be consitent with cv.ra and metaDb
• src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb
  • lines changed 1, context: html, text, full: html, text
    ignore mac resource forks ._* when processing un-archived files
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 39, context: html, text, full: html, text
    fix problem with mouse cell types not getting the org right
  • lines changed 9, context: html, text, full: html, text
    is hoping that eventually he can fix this. Need to filter on organism .
• src/hg/encode/paraMd5sum/paraMd5sum
  • lines changed 38, context: html, text, full: html, text
    script can now ssh to head node to run para
• src/hg/hgApi/hgApi.c
  • lines changed 26, context: html, text, full: html, text
    Metadata link '...' is now populated by ajax
• src/hg/hgCustom/hgCustom.c
  • lines changed 15, context: html, text, full: html, text
    add measureTiming CGI option to measure custom track loading time
  • lines changed 2, context: html, text, full: html, text
    a couple of routines can be static
• src/hg/hgGenome/import.c
  • lines changed 2, context: html, text, full: html, text
    fix a bug where if Jim's regulation multi-wiggles were selected, core was dumped
• src/hg/hgTracks/bamTrack.c
  • lines changed 3, context: html, text, full: html, text
    if the color mode is off, default to using the track color specified in trackDb
• src/hg/hgTracks/config.c
  • lines changed 18, context: html, text, full: html, text
    Drag reorder did nto respect old group reordering or moves from one group to another. This is a fix. NOTE, the ugly ifdefs should be cleaned up soon when all dragReorder ifdefs are cleaned up
• src/hg/hgTracks/hgTracks.c
  • lines changed 12, context: html, text, full: html, text
    Drag reorder did nto respect old group reordering or moves from one group to another. This is a fix. NOTE, the ugly ifdefs should be cleaned up soon when all dragReorder ifdefs are cleaned up
• src/hg/hgTracks/hgTracks.h
  • lines changed 4, context: html, text, full: html, text
    Drag reorder did nto respect old group reordering or moves from one group to another. This is a fix. NOTE, the ugly ifdefs should be cleaned up soon when all dragReorder ifdefs are cleaned up
• src/hg/hgTracks/searchTracks.c
  • lines changed 73, context: html, text, full: html, text
    Added clear button and fixed bombing simple search, among other things
  • lines changed 1, context: html, text, full: html, text
    Removed comment about broken val drop-down update.
  • lines changed 2, context: html, text, full: html, text
    Added to the suggested improvements list the white-listing of mdb vars.
  • lines changed 142, context: html, text, full: html, text
    Created a preliminary white list for mdb vars
  • lines changed 3, context: html, text, full: html, text
    Updated 'recently done' list
  • lines changed 1, context: html, text, full: html, text
    Kate caught my typo
• src/hg/hgTracks/simpleTracks.c
  • lines changed 3, context: html, text, full: html, text
    do not check for base coloring if itemRgb is on
  • lines changed 8, context: html, text, full: html, text
    Fixed view vis toggle bug that Kate complained about
  • lines changed 2, context: html, text, full: html, text
    Assert was invalid for right-clcik update of single track
• src/hg/hgTracks/wigTrack.c
  • lines changed 14, context: html, text, full: html, text
    fix extra useless reading of data blocks when not really necessary
• src/hg/hgc/hgc.c
  • lines changed 104, context: html, text, full: html, text
    NumtS tracks
  • lines changed 6, context: html, text, full: html, text
    description page format
• src/hg/htdocs/ENCODE/index.html
  • lines changed 161, context: html, text, full: html, text
    added Regulation track announcement, collapsed the last two full announcements, removed two archived items
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 121, context: html, text, full: html, text
    added Regulation track announcement, collapsed the last two full announcements, removed two archived items
• 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 1, context: html, text, full: html, text
    "Encode release log update"
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 35, context: html, text, full: html, text
    Added 18 August 2010 - Cat Genome Browser Available and removed a dash in a comment to make the colors in my browser appear
• src/hg/htdocs/goldenPath/releaseLog.html
  • lines changed 168, 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 1, context: html, text, full: html, text
    "Release log update"
• src/hg/htdocs/images/encodeRegShot.gif
  • lines changed 0, context: html, text, full: html, text
    adding image to use in the ENCODE Regulation track announcement
• src/hg/htdocs/indexNews.html
  • lines changed 67, context: html, text, full: html, text
    added Donna's regulation track announcement, minimized the most recentannouncement and removed the oldest announcement
  • lines changed 3, context: html, text, full: html, text
    centered the image and added a border using css
• src/hg/htdocs/style/ENStyle.css
  • lines changed 142, context: html, text, full: html, text
    Starting on an ENCODE specific style sheet.
  • lines changed 142, context: html, text, full: html, text
    Taking this out of main branch. ENCODE Portal changes should now just be on purplePortal local branch. Revert "Starting on an ENCODE specific style sheet." This reverts commit 327e6f818033d8bc0114d944a7b4e2433bc9c79b.
• src/hg/htdocs/style/jquery-ui.css
  • lines changed 4, context: html, text, full: html, text
    Is css ever just so?
• src/hg/inc/hui.h
  • lines changed 5, context: html, text, full: html, text
    Metadata link '...' is now populated by ajax
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    "New version number v239"
• src/hg/js/ajax.js
  • lines changed 13, context: html, text, full: html, text
    Needed to change cfg popup return, because ajaxing over vars then fetching new track had timing issues
  • lines changed 29, context: html, text, full: html, text
    Metadata link '...' is now populated by ajax
• src/hg/js/hgTracks.js
  • lines changed 93, context: html, text, full: html, text
    Added clear button and fixed bombing simple search, among other things
  • lines changed 1, context: html, text, full: html, text
    Newly populated val dropdowns should enable searching
  • lines changed 29, context: html, text, full: html, text
    Fixed some problems with right-click and persistence when hiding subtracks
  • lines changed 30, context: html, text, full: html, text
    Needed to change cfg popup return, because ajaxing over vars then fetching new track had timing issues
  • lines changed 2, context: html, text, full: html, text
    And one more thing. When tracks ar hidden, the image buttons need to be reset
  • lines changed 6, context: html, text, full: html, text
    add hideLoadingImage
  • lines changed 4, context: html, text, full: html, text
    make sure selectedMenuItem is defined before adding configure menu item in loadContextMenu
  • lines changed 2, context: html, text, full: html, text
    fix off-by-one error in getDna
  • lines changed 2, context: html, text, full: html, text
    Cfg popups should not be resizable
• src/hg/js/hui.js
  • lines changed 63, context: html, text, full: html, text
    Checking in work on making hgTrackUi subtrack cfg work by popup just as right-click does. This is ifdef'd out.
  • lines changed 9, context: html, text, full: html, text
    Subtrack list drag and drop needed to use a dragHandle to stop irritating people with green highlighting quite so much. No ideal dragHandle exists, so using checkbox with a bit of padding
• src/hg/js/utils.js
  • lines changed 13, context: html, text, full: html, text
    Fixed some problems with right-click and persistence when hiding subtracks
  • lines changed 34, context: html, text, full: html, text
    Needed to change cfg popup return, because ajaxing over vars then fetching new track had timing issues
  • lines changed 3, context: html, text, full: html, text
    support checkboxes in getAllVarsAsUrlData
  • lines changed 10, context: html, text, full: html, text
    Metadata link '...' is now populated by ajax
• src/hg/lib/cart.c
  • lines changed 2, context: html, text, full: html, text
    Metadata link '...' is now populated by ajax
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    put fileIndex after fileName in ENCODE "..." stanzas. Make into a download link.
  • lines changed 40, context: html, text, full: html, text
    Checking in work on making hgTrackUi subtrack cfg work by popup just as right-click does. This is ifdef'd out.
  • lines changed 61, context: html, text, full: html, text
    Metadata link '...' is now populated by ajax
  • lines changed 14, context: html, text, full: html, text
    Subtrack list drag and drop needed to use a dragHandle to stop irritating people with green highlighting quite so much. No ideal dragHandle exists, so using checkbox with a bit of padding
• src/hg/makeDb/doc/calJac3.txt
  • lines changed 25, context: html, text, full: html, text
    DONE phastCons 13-way
• src/hg/makeDb/doc/dm2.txt
  • lines changed 71, context: html, text, full: html, text
    Adding new composite track BDTNP DNase, and new subtracks for BDTNP ChIP/chip. Since composite labels are no longer displayed above subtracks in hgTracks, I added track shortLabel to the beginning of subtrack longLabels.
  • lines changed 23, context: html, text, full: html, text
    Replaced BDTNP DNase bigWigs w/normalized data from Mark Biggin.
• src/hg/makeDb/doc/encodeDccHg18/broadBernstein.txt
  • lines changed 747, context: html, text, full: html, text
    Doc files that should have been checked in months ago. Also hg19 documentation should be moved to hg19 specific doc files
• src/hg/makeDb/doc/encodeDccHg18/dukeUtaUncCrawford.txt
  • lines changed 968, context: html, text, full: html, text
    Doc files that should have been checked in months ago. Also hg19 documentation should be moved to hg19 specific doc files
• src/hg/makeDb/doc/encodeDccHg18/haibChipSeq.txt
  • lines changed 177, context: html, text, full: html, text
    Doc files that should have been checked in months ago. Also hg19 documentation should be moved to hg19 specific doc files
• src/hg/makeDb/doc/encodeDccHg18/uwStam.txt
  • lines changed 512, context: html, text, full: html, text
    Doc files that should have been checked in months ago. Also hg19 documentation should be moved to hg19 specific doc files
• src/hg/makeDb/doc/encodeDccHg18/yaleDavisHarvardSnyder.txt
  • lines changed 147, context: html, text, full: html, text
    Doc files that should have been checked in months ago. Also hg19 documentation should be moved to hg19 specific doc files
• src/hg/makeDb/doc/felCat3.txt
  • lines changed 5, context: html, text, full: html, text
    felCat3 <-> felCat4 liftOver
• src/hg/makeDb/doc/felCat4.txt
  • lines changed 32, context: html, text, full: html, text
    felCat3 <-> felCat4 liftOver
• src/hg/makeDb/doc/hg18.nt.txt
  • lines changed 1, context: html, text, full: html, text
    Follow-up to d03112c5 -- correct the order of S SNPs ancestral/derived codes in the make doc too.
• src/hg/makeDb/doc/hg18.txt
  • lines changed 23, context: html, text, full: html, text
    numtS track
• src/hg/makeDb/doc/hg19.txt
  • lines changed 176, context: html, text, full: html, text
    beginning of altSequence track and Vega gene update v39 done
• src/hg/makeDb/doc/hg19Patch2.txt
  • lines changed 209, context: html, text, full: html, text
    initial contents for hg19 Patch2
  • lines changed 154, context: html, text, full: html, text
    adding ctgPos, ctgPos2, altSequence, and running genbank
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added hg19Patch2 - Human - GRCh37.p2
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 23, context: html, text, full: html, text
    adding hg19Patch2
  • lines changed 1, context: html, text, full: html, text
    need lift file for hg19Patch2
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added hg19Patch2 - Human - GRCh37.p2
• src/hg/makeDb/genbank/etc/ignore.idx
  • lines changed 125, context: html, text, full: html, text
    added ignore entries for pig name change
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 1, context: html, text, full: html, text
    added new name for domestic pig to list of alternatives
• src/hg/makeDb/hgBbiDbLink/hgBbiDbLink.c
  • lines changed 2, context: html, text, full: html, text
    Add 'drop table if exists' before create, for those of us who have to run this command more than once sometimes. :)
• src/hg/makeDb/mdbUpdate/mdbPrint.c
  • lines changed 14, context: html, text, full: html, text
    Minor cleanup of mdbPrint code which is only used by wranglers
• src/hg/makeDb/trackDb/README
  • lines changed 61, context: html, text, full: html, text
    Adding container tracks info to trackDb/README.
• src/hg/makeDb/trackDb/drosophila/trackDb.ra
  • lines changed 421, context: html, text, full: html, text
    Adding new composite track BDTNP DNase, and new subtracks for BDTNP ChIP/chip. Since composite labels are no longer displayed above subtracks in hgTracks, I added track shortLabel to the beginning of subtrack longLabels.
  • lines changed 11, context: html, text, full: html, text
    Replaced BDTNP DNase bigWigs w/normalized data from Mark Biggin.
• src/hg/makeDb/trackDb/human/altSequence.html
  • lines changed 16, context: html, text, full: html, text
    adding altSequence to hg19Patch2;
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 973, context: html, text, full: html, text
    Added metaData for fastq's submitted for hg19 forgotten from hg18
  • lines changed 733, context: html, text, full: html, text
    Oops. Added metaData for fastq's correctly this time
  • lines changed 13, context: html, text, full: html, text
    Added 12 localiations for subId=1874
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 2, context: html, text, full: html, text
    Fixed typo in one var
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwChIPSeq.ra
  • lines changed 7, context: html, text, full: html, text
    Fixed 4 vars which had typos
  • lines changed 6, context: html, text, full: html, text
    Fixed some more mispelled vars
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegDnaseClustered.html
  • lines changed 1, context: html, text, full: html, text
    Editing text on DNAse track to be a little more precise.
• src/hg/makeDb/trackDb/human/hg19/altSequence.html
  • lines changed 16, context: html, text, full: html, text
    moving up one level
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 188, context: html, text, full: html, text
    Updated metaData (origAssembly) and trackDb
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 196, context: html, text, full: html, text
    change from bedGraphs to bigWigs
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    bed 9 . will turn on score filters and add scoreFilterByRange
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    adding altSequence to hg19Patch2;
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    naming patch2 alignments as chainHg19 and chainHg19Patch2
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    table chainHg19Patch2 becomes testChainHg19Patch2
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeHaibTfbs.ra
  • lines changed 1, context: html, text, full: html, text
    Updated metaData (origAssembly) and trackDb
• src/hg/makeDb/trackDb/human/hg19/vegaGeneComposite.html
  • lines changed 1, context: html, text, full: html, text
    update comment to include Non-Coding on the description
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.html
  • lines changed 1, context: html, text, full: html, text
    removed dupicated text
  • lines changed 5, context: html, text, full: html, text
    remove the Alignments view
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.ra
  • lines changed 107, context: html, text, full: html, text
    remove the Alignments view
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    make bamColorMode be off by default so ENCODE cell colors are displayed
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    take view out of sortOrder since it's not here anymore (fixes (null) header)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.html
  • lines changed 135, context: html, text, full: html, text
    begin the GisRnaPet track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
  • lines changed 253, context: html, text, full: html, text
    begin the GisRnaPet track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.ra
  • lines changed 124, context: html, text, full: html, text
    change from bedGraphs to bigWigs
• src/hg/makeDb/trackDb/human/hg19Patch2/description.html
  • lines changed 129, context: html, text, full: html, text
    initial files for hg19Patch2
  • lines changed 216, context: html, text, full: html, text
    update documents to hg19 status and adding ctgPos2 track to trackDb.ra
• src/hg/makeDb/trackDb/human/hg19Patch2/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial files for hg19Patch2
  • lines changed 68, context: html, text, full: html, text
    update documents to hg19 status and adding ctgPos2 track to trackDb.ra
• src/hg/makeDb/trackDb/human/hg19Patch2/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial files for hg19Patch2
  • lines changed 38, context: html, text, full: html, text
    update documents to hg19 status and adding ctgPos2 track to trackDb.ra
• src/hg/makeDb/trackDb/human/hg19Patch2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files for hg19Patch2
  • lines changed 7, context: html, text, full: html, text
    update documents to hg19 status and adding ctgPos2 track to trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    adding altSequence to hg19Patch2;
  • lines changed 12, context: html, text, full: html, text
    naming patch2 alignments as chainHg19 and chainHg19Patch2
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    chainHg19 to be replaced now called testChainHg19
• src/hg/makeDb/trackDb/human/ntModernHumans.html
  • lines changed 2, context: html, text, full: html, text
    [MLQ #763 inconsistency with Neandertal Selection Sweep Scan display]: user found that ntSss description had Papuan and Han in the wrong order, confirmed by Ed Green. Swapped them back and also put the modern human BAM in the same order as the ntSss codes.
• src/hg/makeDb/trackDb/human/ntSssSnps.html
  • lines changed 2, context: html, text, full: html, text
    [MLQ #763 inconsistency with Neandertal Selection Sweep Scan display]: user found that ntSss description had Papuan and Han in the wrong order, confirmed by Ed Green. Swapped them back and also put the modern human BAM in the same order as the ntSss codes.
• src/hg/makeDb/trackDb/human/trackDb.nt.ra
  • lines changed 7, context: html, text, full: html, text
    [MLQ #763 inconsistency with Neandertal Selection Sweep Scan display]: user found that ntSss description had Papuan and Han in the wrong order, confirmed by Ed Green. Swapped them back and also put the modern human BAM in the same order as the ntSss codes.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    no need for a naked chainHg19 table definition here
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding hg19Patch2 to the build
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 51, context: html, text, full: html, text
    adding chainNetHg19Patch2 definition
• src/hg/utils/automation/HgAutomate.pm
  • lines changed 1, context: html, text, full: html, text
    using /scratch/data instead of /hive/data/genomes
• src/hg/utils/automation/doEnsGeneUpdate.pl
  • lines changed 5, context: html, text, full: html, text
    update human vegaGene peptide file name for version 39 human vega release
• src/hg/utils/automation/doSameSpeciesLiftOver.pl
  • lines changed 1, context: html, text, full: html, text
    do not use expr, use awk instead
  • lines changed 2, context: html, text, full: html, text
    do not use expr, use awk instead
  • lines changed 4, context: html, text, full: html, text
    using /scratch/data instead of /hive/data/genomes
  • lines changed 9, context: html, text, full: html, text
    must force /scratch/data for sequences ?
• src/hg/utils/makeTrackIndex/makeTrackIndex.c
  • lines changed 7, context: html, text, full: html, text
    index targetDescription too
• src/hg/utils/makeTrackIndex/makefile
  • lines changed 7, context: html, text, full: html, text
    add build target to build an index for an assembly (probably temporary until we integrate into trackDb build)
• src/hg/utils/mutationClassifier/mutationClassifier.c
  • lines changed 58, context: html, text, full: html, text
    tweak parseSnp; support maxDelta == 0
• src/makefile
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    adding gff3ToGenePred
• src/utils/git-reports/git-reports.c
  • lines changed 6, context: html, text, full: html, text
    Putting commits in chronological order in git-reports.
• src/utils/git-reports/makefile
  • lines changed 2, context: html, text, full: html, text
    fixing test target for executable and correct date range
• src/utils/qa/weeklybld/buildEnv.csh
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    v239 final build

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• files changed: 161