All File Changes

v246_preview to v246_preview2 (2011-01-11 to 2011-01-18) v246

• python/ucscGenomics/__init__.py
  • lines changed 0, context: html, text, full: html, text
    Moved Python Modules source to live under kent/python/ucscGenomics to be equivalent to java directory.
• python/ucscGenomics/styleGuide.txt
  • lines changed 2, context: html, text, full: html, text
    Moved Python Modules source to live under kent/python/ucscGenomics to be equivalent to java directory.
• src/hg/altSplice/altSplice/genePredToPsl.c
  • lines changed 23, context: html, text, full: html, text
    Changed db parameter to be a chrom.sizes file, which is the preferred choice these days (since about 2005 anyway)
• src/hg/encode/DAFs/2.0/haibCnv.daf
  • lines changed 9, context: html, text, full: html, text
    DAFs in progress with HAIB
• src/hg/encode/DAFs/2.0/haibRnaSeq.daf
  • lines changed 29, context: html, text, full: html, text
    DAFs in progress with HAIB
• src/hg/encode/DAFs/2.0/stanfordHg19Tfbs.daf
  • lines changed 2, context: html, text, full: html, text
    Added bam validation, that seems to have disapeard from daf.
• src/hg/encode/DAFs/2.0/uncBsuProt.daf
  • lines changed 1, context: html, text, full: html, text
    Shortened the compositeSuffix from uncBsuProtgeno to uncBsuProt, after learning that their metadata includes localization as well as cell type. Shortening the composite name allows us to build short labels that still contain some recognizable (hopefully) representation of this metadata
• src/hg/encode/DAFs/2.0/uwExonArray.daf
  • lines changed 12, context: html, text, full: html, text
    UW submitted another 23 files representing 13 experiments. One of those experiments had a treatment. I added treatment and fixed UW in the .daf file. I added tracks and fixed long/short labels in .ra file. I added metadata in the alpha.ra files. I added a sentace about the treatment in the .html. I updated the notes file.
• src/hg/encode/autoSql/bedLogR.as
  • lines changed 14, context: html, text, full: html, text
    for HAIB CNV data
• src/hg/encode/autoSql/bedLogR.sql
  • lines changed 22, context: html, text, full: html, text
    for HAIB CNV data
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 6, context: html, text, full: html, text
    Bed files should be named as .bed.gz not .bed9+.gz
• src/hg/encode/encodeValidate/config/expVars.ra
  • lines changed 1, context: html, text, full: html, text
    typo
• src/hg/encode/encodeValidate/config/labs.ra
  • lines changed 3, context: html, text, full: html, text
    add Ruan lab
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 1, context: html, text, full: html, text
    add bedLogR
  • lines changed 1, context: html, text, full: html, text
    Bed files should be named as .bed.gz not .bed9+.gz
  • lines changed 1, context: html, text, full: html, text
    Added further comments about adding obtainedBy into the subGroups.
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    put file name in quotes so it can have special characters in it
• src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeCshlLongRnaSeq.hg18.soft
  • lines changed 111, context: html, text, full: html, text
    GEO metadata and SOFT file for CSHL Long (hg18)
• src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeUwDgf.hg19.soft
  • lines changed 448, context: html, text, full: html, text
    GEO metadata and SOFT file for UW DGF
• src/hg/encode/inc/bedLogR.h
  • lines changed 70, context: html, text, full: html, text
    for HAIB CNV data
• src/hg/encode/lib/bedLogR.c
  • lines changed 166, context: html, text, full: html, text
    for HAIB CNV data
• src/hg/genePredToGtf/genePredToGtf.c
  • lines changed 4, context: html, text, full: html, text
    clarified doc
• src/hg/genePredToGtf/makefile
  • lines changed 2, context: html, text, full: html, text
    need to have DESTDIR in there
  • lines changed 10, context: html, text, full: html, text
    using DESTDIR so this can be a userApp
• src/hg/hgFileUi/hgFileUi.c
  • lines changed 7, context: html, text, full: html, text
    hgFileUi no longer depends upon a fileSortOrder setting
• src/hg/hgGene/hgGene.c
  • lines changed 27, context: html, text, full: html, text
    Added logic of hgg_gene search for OMIM gene symbol.
• src/hg/hgTables/bigBed.c
  • lines changed 6, context: html, text, full: html, text
    Starting to work on getting bigBeds from data hubs to work with table browser. Still a ways to go though.
• src/hg/hgTables/bigWig.c
  • lines changed 14, context: html, text, full: html, text
    Starting to integrate data hub into table browser. Still problems, so effectively is commented out at the moment.
  • lines changed 2, context: html, text, full: html, text
    Making hub work with table browser.
• src/hg/hgTables/hgTables.c
  • lines changed 54, context: html, text, full: html, text
    Starting to integrate data hub into table browser. Still problems, so effectively is commented out at the moment.
  • lines changed 50, context: html, text, full: html, text
    Making hub work with table browser.
  • lines changed 1, context: html, text, full: html, text
    Fixing hgTracks so that hub is in it's own group again. Broke this with some efforts to get things going in hgTables.
  • lines changed 18, context: html, text, full: html, text
    Starting to work on getting bigBeds from data hubs to work with table browser. Still a ways to go though.
• src/hg/hgTables/hgTables.h
  • lines changed 5, context: html, text, full: html, text
    Starting to integrate data hub into table browser. Still problems, so effectively is commented out at the moment.
  • lines changed 1, context: html, text, full: html, text
    Making hub work with table browser.
• src/hg/hgTables/mainPage.c
  • lines changed 2, context: html, text, full: html, text
    Starting to integrate data hub into table browser. Still problems, so effectively is commented out at the moment.
• src/hg/hgTables/schema.c
  • lines changed 13, context: html, text, full: html, text
    Making hub work with table browser.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 24, context: html, text, full: html, text
    Made several portions of the SNP controls page collapsible.
  • lines changed 20, context: html, text, full: html, text
    Adding hub support to hgc.
  • lines changed 3, context: html, text, full: html, text
    set canPack to TRUE for wikiTracks (redmine 2395)
• src/hg/hgTracks/cds.c
  • lines changed 4, context: html, text, full: html, text
    Added some #ifdef USE_BAM's to fix compile on systems that don't have samtools/USE_BAM.
• src/hg/hgTracks/cds.h
  • lines changed 4, context: html, text, full: html, text
    Added some #ifdef USE_BAM's to fix compile on systems that don't have samtools/USE_BAM.
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    Fixing compile problem. Oops, sorry, thought I had tested it all....
  • lines changed 3, context: html, text, full: html, text
    Fixing hgTracks so that hub is in it's own group again. Broke this with some efforts to get things going in hgTables.
• src/hg/hgTracks/searchTracks.c
  • lines changed 269, context: html, text, full: html, text
    Checked in file search tab but ifdef'd out
• src/hg/hgTracks/simpleTracks.c
  • lines changed 3, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): registered track handlers for new subset tracks snp132Common, snp132Patient, snp132NonUnique.
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    Small bugfix and format tweak for SNP details when there are multiplemappings to the genome.
  • lines changed 36, context: html, text, full: html, text
    Moved hgc.c's {begin,end}CollapsibleSection to jsHelper.c:js{Begin,End}CollapsibleSection so I can use in hgTrackUi.
  • lines changed 4, context: html, text, full: html, text
    Some more polishing for SNP details.
  • lines changed 6, context: html, text, full: html, text
    Adding hub support to hgc.
  • lines changed 1, context: html, text, full: html, text
    Fixing hgTracks so that hub is in it's own group again. Broke this with some efforts to get things going in hgTables.
  • lines changed 5, context: html, text, full: html, text
    Just for fun, added HGDP world map icon to collapsible section header in SNP details.
• src/hg/hgc/hgc.h
  • lines changed 4, context: html, text, full: html, text
    Oops, thought this was included in 31b56093: Just for fun, added HGDP world map icon to collapsible section header in SNP details.
• src/hg/hgc/hgdpClick.c
  • lines changed 26, context: html, text, full: html, text
    Just for fun, added HGDP world map icon to collapsible section header in SNP details.
• src/hg/hgc/wiggleClick.c
  • lines changed 5, context: html, text, full: html, text
    Fixing hgTracks so that hub is in it's own group again. Broke this with some efforts to get things going in hgTables.
• src/hg/htdocs/ENCODE/aboutScaleup.html
  • lines changed 84, context: html, text, full: html, text
    Overflow for About ENCODE section to unclutter main page
  • lines changed 2, context: html, text, full: html, text
    Portal update to address input from PI's. Lighten up 'About' section, adding/highlighting critical info and links. Add 'Data Summary' pages for Human and Mouse. Point to preview browser. Reorder blue bar menu items.
• src/hg/htdocs/ENCODE/dataPlansMouse.html
  • lines changed 93, context: html, text, full: html, text
    Add Mouse data plans page
• src/hg/htdocs/ENCODE/dataSummary.html
  • lines changed 90, context: html, text, full: html, text
    First cut of data summary files. Need to commit immediately for make to pick them up and stage in apache dir
  • lines changed 34, context: html, text, full: html, text
    Portal update to address input from PI's. Lighten up 'About' section, adding/highlighting critical info and links. Add 'Data Summary' pages for Human and Mouse. Point to preview browser. Reorder blue bar menu items.
• src/hg/htdocs/ENCODE/dataSummaryMouse.html
  • lines changed 92, context: html, text, full: html, text
    First cut of data summary files. Need to commit immediately for make to pick them up and stage in apache dir
  • lines changed 36, context: html, text, full: html, text
    Portal update to address input from PI's. Lighten up 'About' section, adding/highlighting critical info and links. Add 'Data Summary' pages for Human and Mouse. Point to preview browser. Reorder blue bar menu items.
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 1, context: html, text, full: html, text
    fixing a typo, code review Redmine issue #2162
• src/hg/htdocs/ENCODE/index.html
  • lines changed 1, context: html, text, full: html, text
    More informative title for News item
  • lines changed 81, context: html, text, full: html, text
    Portal update to address input from PI's. Lighten up 'About' section, adding/highlighting critical info and links. Add 'Data Summary' pages for Human and Mouse. Point to preview browser. Reorder blue bar menu items.
  • lines changed 37, context: html, text, full: html, text
    Update color scheme to less UCSC, more ENCODE-logo related
  • lines changed 8, context: html, text, full: html, text
    Add graphic from Nature paper
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 2, context: html, text, full: html, text
    Added danRer7 release info.
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 3, context: html, text, full: html, text
    Added danRer7.
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 2, context: html, text, full: html, text
    added direct link to description text template instead of merely telling them where on the site to click
  • lines changed 2, context: html, text, full: html, text
    added direct link to description text template instead of merely telling them where on the site to click
• src/hg/htdocs/goldenPath/help/hg18ToHg19LiftOver.html
  • lines changed 1, context: html, text, full: html, text
    reworded per Mary's suggestion. shortened a long sentence
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 55, context: html, text, full: html, text
    Announcement and help mods for right-click.
• src/hg/htdocs/images/rightclick.png
  • lines changed 0, context: html, text, full: html, text
    Announcement and help mods for right-click.
• src/hg/htdocs/indexNews.html
  • lines changed 76, context: html, text, full: html, text
    Announcement and help mods for right-click.
  • lines changed 1, context: html, text, full: html, text
    Rats, forgot to change the png file name.
• src/hg/htdocs/style/ENStyle.css
  • lines changed 238, context: html, text, full: html, text
    First cut ENCODE portal style sheet
• src/hg/htdocs/style/HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    CSS tweak: added class=bigBlue to TD in beginCollapsibleSection
• src/hg/inc/fileUi.h
  • lines changed 4, context: html, text, full: html, text
    Added suppport for file searching
• src/hg/inc/hubConnect.h
  • lines changed 6, context: html, text, full: html, text
    Adding hub support to hgc.
  • lines changed 1, context: html, text, full: html, text
    Starting to integrate data hub into table browser. Still problems, so effectively is commented out at the moment.
• src/hg/inc/jsHelper.h
  • lines changed 8, context: html, text, full: html, text
    Moved hgc.c's {begin,end}CollapsibleSection to jsHelper.c:js{Begin,End}CollapsibleSection so I can use in hgTrackUi.
• src/hg/inc/mdb.h
  • lines changed 27, context: html, text, full: html, text
    Added suppport for file searching
  • lines changed 10, context: html, text, full: html, text
    Added some support routines for file searching/sorting code
• src/hg/inc/peptideMapping.h
  • lines changed 1, context: html, text, full: html, text
    Updated peptideMapping.h after revising peptideMapping.as and peptideMapping.sql. See the comments on those commits
• src/hg/inc/trackHub.h
  • lines changed 3, context: html, text, full: html, text
    Fixing hgTracks so that hub is in it's own group again. Broke this with some efforts to get things going in hgTables.
• src/hg/inc/wgEncodeGencodeExonSupport.h
  • lines changed 62, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/inc/wgEncodeGencodeGeneSymbol.h
  • lines changed 62, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/inc/wgEncodeGencodePdb.h
  • lines changed 62, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/inc/wgEncodeGencodePubmed.h
  • lines changed 62, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/inc/wgEncodeGencodeRefSeq.h
  • lines changed 63, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/inc/wgEncodeGencodeSource.h
  • lines changed 68, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/inc/wgEncodeGencodeTranscriptSupport.h
  • lines changed 62, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/inc/wgEncodeGencodeUniProt.h
  • lines changed 62, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/js/hgTracks.js
  • lines changed 12, context: html, text, full: html, text
    Added support for hiding found files or tracks when switching tabs on search page
  • lines changed 43, context: html, text, full: html, text
    fix problems with zoomed-out microarray tracks (redmine 2447); also include some experimental floating item code (currently dead code)
• src/hg/lib/customFactory.c
  • lines changed 52, context: html, text, full: html, text
    fixing some of the easy memory leaks
  • lines changed 22, context: html, text, full: html, text
    a few more leaks stamped out
• src/hg/lib/customTrack.c
  • lines changed 1, context: html, text, full: html, text
    fixing some of the easy memory leaks
• src/hg/lib/encode/peptideMapping.as
  • lines changed 1, context: html, text, full: html, text
    At the request of the Giddings lab, changed the precursor Mz field to a generic spectrum ID field. The purpose of the precursor Mz field was to act as an internal identifier for the spectrum. In time, they plan to identify spectra through MD5sums instead. Making this field a generically-named string provides the opportunity to accept a wider variety of IDs, including MD5sums as well as precursor Mzs. Also, made a non-unique key that includes the spectrum Id, because it turns out that the precursor Mz is not unique
• src/hg/lib/encode/peptideMapping.c
  • lines changed 5, context: html, text, full: html, text
    I'd forgotten to commit peptideMapping.c along with peptideMapping.as and peptideMapping.sql. See the comments in that commit
• src/hg/lib/encode/peptideMapping.sql
  • lines changed 2, context: html, text, full: html, text
    At the request of the Giddings lab, changed the precursor Mz field to a generic spectrum ID field. The purpose of the precursor Mz field was to act as an internal identifier for the spectrum. In time, they plan to identify spectra through MD5sums instead. Making this field a generically-named string provides the opportunity to accept a wider variety of IDs, including MD5sums as well as precursor Mzs. Also, made a non-unique key that includes the spectrum Id, because it turns out that the precursor Mz is not unique
• src/hg/lib/encode/wgEncodeGencodeExonSupport.as
  • lines changed 6, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodeExonSupport.c
  • lines changed 124, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodeExonSupport.sql
  • lines changed 12, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodeGeneSymbol.as
  • lines changed 6, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodeGeneSymbol.c
  • lines changed 124, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodeGeneSymbol.sql
  • lines changed 12, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodePdb.as
  • lines changed 6, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodePdb.c
  • lines changed 124, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodePdb.sql
  • lines changed 12, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodePubmed.as
  • lines changed 6, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodePubmed.c
  • lines changed 124, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodePubmed.sql
  • lines changed 12, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodeRefSeq.as
  • lines changed 7, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodeRefSeq.c
  • lines changed 132, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodeRefSeq.sql
  • lines changed 13, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodeSource.as
  • lines changed 6, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodeSource.c
  • lines changed 127, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodeSource.sql
  • lines changed 12, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodeTranscriptSupport.as
  • lines changed 6, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodeTranscriptSupport.c
  • lines changed 124, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodeTranscriptSupport.sql
  • lines changed 12, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodeUniProt.as
  • lines changed 6, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodeUniProt.c
  • lines changed 124, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/encode/wgEncodeGencodeUniProt.sql
  • lines changed 12, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/fileUi.c
  • lines changed 241, context: html, text, full: html, text
    Added suppport for file searching
  • lines changed 14, context: html, text, full: html, text
    dateUnrestricted should be grey not hidden, when file is already ripened.
  • lines changed 484, context: html, text, full: html, text
    Added a default sort order. Special code to find .bai files. Common sortable table for both hgFileUi and fileSearch. Added folder link to hgFileUi from file search.
  • lines changed 6, context: html, text, full: html, text
    Rearranged the defaulting sort order fields slightly
  • lines changed 6, context: html, text, full: html, text
    And a little more tweeking. Don't create a default column when all values will be the same
  • lines changed 9, context: html, text, full: html, text
    Really must stop trying things and wait for feedback
• src/hg/lib/hgFind.c
  • lines changed 1, context: html, text, full: html, text
    Small fix: pass a proper format string to truncatef because the string to be copied can contain '%'.
• src/hg/lib/hubConnect.c
  • lines changed 33, context: html, text, full: html, text
    Adding hub support to hgc.
  • lines changed 1, context: html, text, full: html, text
    Starting to integrate data hub into table browser. Still problems, so effectively is commented out at the moment.
  • lines changed 1, context: html, text, full: html, text
    Fixing hgTracks so that hub is in it's own group again. Broke this with some efforts to get things going in hgTables.
• src/hg/lib/hubConnect.sql
  • lines changed 4, context: html, text, full: html, text
    Fixing comment.
• src/hg/lib/jsHelper.c
  • lines changed 31, context: html, text, full: html, text
    Moved hgc.c's {begin,end}CollapsibleSection to jsHelper.c:js{Begin,End}CollapsibleSection so I can use in hgTrackUi.
  • lines changed 1, context: html, text, full: html, text
    Added width to <TD> tag in jsBeginCollapsible section. This stabilizes the width in FireFox but unfortunately not IE.
  • lines changed 1, context: html, text, full: html, text
    CSS tweak: added class=bigBlue to TD in beginCollapsibleSection
• src/hg/lib/makefile
  • lines changed 4, context: html, text, full: html, text
    gencode metadata autoSql
• src/hg/lib/mdb.c
  • lines changed 232, context: html, text, full: html, text
    Added suppport for file searching
  • lines changed 52, context: html, text, full: html, text
    Added some support routines for file searching/sorting code
• src/hg/lib/omimGeneMap.sql
  • lines changed 22, context: html, text, full: html, text
    changed disordersN fields to blob instead of varchar(255)
• src/hg/lib/trackHub.c
  • lines changed 5, context: html, text, full: html, text
    Starting to integrate data hub into table browser. Still problems, so effectively is commented out at the moment.
  • lines changed 5, context: html, text, full: html, text
    Fixing hgTracks so that hub is in it's own group again. Broke this with some efforts to get things going in hgTables.
• src/hg/makeDb/doc/calJac3.txt
  • lines changed 2, context: html, text, full: html, text
    Create liftOver files to and from: calJac3 <-> hg18
• src/hg/makeDb/doc/droVir3.txt
  • lines changed 39, context: html, text, full: html, text
    Create droVir3toDroVir2.over.chain.gz file
• src/hg/makeDb/doc/encodeDccHg19/openChromCrawford.hg19.txt
  • lines changed 629, context: html, text, full: html, text
    Wrangling OpenChrom
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeBuOrchid.release1.notes
  • lines changed 50, context: html, text, full: html, text
    Change Notes for BU ORChID
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwAffyExonArray.release1.notes
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    UW submitted another 23 files representing 13 experiments. One of those experiments had a treatment. I added treatment and fixed UW in the .daf file. I added tracks and fixed long/short labels in .ra file. I added metadata in the alpha.ra files. I added a sentace about the treatment in the .html. I updated the notes file.
• src/hg/makeDb/doc/hg18.txt
  • lines changed 3, context: html, text, full: html, text
    Create liftOver files to and from: calJac3 <-> hg18
• src/hg/makeDb/doc/hg19.txt
  • lines changed 3, context: html, text, full: html, text
    redmine bug 1685 Trim trailing ; from knownToU133.value
  • lines changed 76, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added subsets of snp132: Common, Patient, Non-Unique ("Failed" for now as Paul Flicek described them)
• src/hg/makeDb/doc/mm9.txt
  • lines changed 13, context: html, text, full: html, text
    Added SEGMENTAL DUPLICATIONS track for mm9.
• src/hg/makeDb/schema/all.joiner
  • lines changed 9, context: html, text, full: html, text
    redmine bug 1685 - joinerCheck error
• src/hg/makeDb/trackDb/buildTrix
  • lines changed 1, context: html, text, full: html, text
    make tmp files easier to track
  • lines changed 5, context: html, text, full: html, text
    fix the "leaving tmp files around" problem
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 119, context: html, text, full: html, text
    Provisionally added seven new cell types for the Stam lab
  • lines changed 3, context: html, text, full: html, text
    Added a couple 'order URLs' for cells that are obtained from an individual rather than a vendor
  • lines changed 32, context: html, text, full: html, text
    Added two new antibodies for HudsonAlpha
  • lines changed 2, context: html, text, full: html, text
    Tweaked the validation doc labels on the two new antibodies, after noticing that any parens in the validation label get stripped out
  • lines changed 6, context: html, text, full: html, text
    Registered new Hydroxytamoxifen for Stam lab.
  • lines changed 7, context: html, text, full: html, text
    Added the membrane fraction localization
  • lines changed 16, context: html, text, full: html, text
    Provisionally added typeOfTerm=privacy and dataType=Combined for openChrom.
  • lines changed 15, context: html, text, full: html, text
    Registered three new treatments. DEX_100pM, EtOH_0.01pct_4hr and EtOH_0.01pct_12hr. They are variations on treatments already registerd.
  • lines changed 1, context: html, text, full: html, text
    Fixed typo in DEX_100pM registration.
  • lines changed 107, context: html, text, full: html, text
    Added six new antibodies
  • lines changed 9, context: html, text, full: html, text
    Selected several provisional stanzas
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 82, context: html, text, full: html, text
    releasing reviewed cv.ra changes to public site
• src/hg/makeDb/trackDb/fishClones.html
  • lines changed 3, context: html, text, full: html, text
    fixed citation
• src/hg/makeDb/trackDb/human/altSeqComposite.html
  • lines changed 3, context: html, text, full: html, text
    adding link to downloads http://redmine.soe.ucsc.edu/issues/1892
  • lines changed 1, context: html, text, full: html, text
    making track lowercase http://redmine.soe.ucsc.edu/issues/2416
• src/hg/makeDb/trackDb/human/denisovaModernHumans.html
  • lines changed 4, context: html, text, full: html, text
    added link to download files
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 16, context: html, text, full: html, text
    GEO metadata and SOFT file for CSHL Long (hg18)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 1691, context: html, text, full: html, text
    added 13 more tracks
  • lines changed 261, context: html, text, full: html, text
    Added 2 more submissions
  • lines changed 91, context: html, text, full: html, text
    change dataType
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 50, context: html, text, full: html, text
    added GEO accessions for hg19 version of wgEncodeCshlShortRnaSeq
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 342, context: html, text, full: html, text
    remove cruft in mdb, see issue 2373
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 20, context: html, text, full: html, text
    Mark some cell lines as private=noSequence
  • lines changed 20, context: html, text, full: html, text
    Added in missing fileIndex refs and a couple more DNase were marked as privacy=noSequence
  • lines changed 4, context: html, text, full: html, text
    Peaks and Signals resubmitted for K562 CTCF and Pol2
  • lines changed 2, context: html, text, full: html, text
    Missed one
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 56, context: html, text, full: html, text
    Mark some cell lines as private=noSequence
  • lines changed 61, context: html, text, full: html, text
    Added in missing fileIndex refs and a couple more DNase were marked as privacy=noSequence
  • lines changed 36, context: html, text, full: html, text
    Found 2 missing fastqs
  • lines changed 246, context: html, text, full: html, text
    Two more experiments added
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 155, context: html, text, full: html, text
    Removed revoked objects
  • lines changed 16, context: html, text, full: html, text
    Added in missing fileIndex refs and a couple more DNase were marked as privacy=noSequence
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
  • lines changed 442, context: html, text, full: html, text
    UW submitted another 23 files representing 13 experiments. One of those experiments had a treatment. I added treatment and fixed UW in the .daf file. I added tracks and fixed long/short labels in .ra file. I added metadata in the alpha.ra files. I added a sentace about the treatment in the .html. I updated the notes file.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 78, context: html, text, full: html, text
    GEO metadata and SOFT file for UW DGF
  • lines changed 729, context: html, text, full: html, text
    Added 7 experiments for the Jan 2011 Freeze.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 3736, context: html, text, full: html, text
    Added data for the Jan Freeze. Should be all of the expected data submissions.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 11546, context: html, text, full: html, text
    Removed meta-data for 2 extraneous fastq files from hg18 that do not have corresponding experiments.
  • lines changed 11504, context: html, text, full: html, text
    Fixed error in commit 6e3f7209efb4a004797ce545f18222b810167b91 by correctly removing metaData for extraneous fastq files.
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging metadata on beta for Broad Histone
  • lines changed 2, context: html, text, full: html, text
    staging Riken Cage metaDb, redmine issue #41
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeBroadHistone.ra
  • lines changed 21085, context: html, text, full: html, text
    staging metadata on beta for Broad Histone
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlShortRnaSeq.ra
  • lines changed 125, context: html, text, full: html, text
    staging metadata changes to add Geo info (#2057) and changing other changes Cricket made including changing short to shortTotal which was requested by the lab
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRikenCage.ra
  • lines changed 5206, context: html, text, full: html, text
    staging Riken Cage metaDb, redmine issue #41
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    added pennantIcon for switchDbTss to indicate it is lifted
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 7, context: html, text, full: html, text
    Added data for the Jan Freeze. Should be all of the expected data submissions.
  • lines changed 2, context: html, text, full: html, text
    Added 7 experiments for the Jan 2011 Freeze.
  • lines changed 10, context: html, text, full: html, text
    removed alpha lines from wgEncodeBroadHistone.ra; moved wgEncodeBroadHistone (added alpha,beta release tag) & wgEncodeMethulRrbs include statements to separate sections
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.ra
  • lines changed 289, context: html, text, full: html, text
    removed alpha lines from wgEncodeBroadHistone.ra; moved wgEncodeBroadHistone (added alpha,beta release tag) & wgEncodeMethulRrbs include statements to separate sections
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
  • lines changed 721, context: html, text, full: html, text
    added 13 more tracks to CSHL long
  • lines changed 89, context: html, text, full: html, text
    Added 2 more submissions
  • lines changed 637, context: html, text, full: html, text
    long label changes, removing SUSPECT DATA from HUVEC and adding to HeLa
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra
  • lines changed 132, context: html, text, full: html, text
    Another round of smoothing lable problems
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra
  • lines changed 328, context: html, text, full: html, text
    Added 2 experiments and cleaned up some labelling
  • lines changed 53, context: html, text, full: html, text
    Another round of smoothing lable problems
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra
  • lines changed 127, context: html, text, full: html, text
    Another round of smoothing lable problems
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.ra
  • lines changed 184, context: html, text, full: html, text
    staging Riken Cage, redmine issue #41
  • lines changed 1, context: html, text, full: html, text
    wgEncodeRikenCageK562NucleolusTotalAlnRep1 changed the short label to fit the length
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.html
  • lines changed 4, context: html, text, full: html, text
    UW submitted another 23 files representing 13 experiments. One of those experiments had a treatment. I added treatment and fixed UW in the .daf file. I added tracks and fixed long/short labels in .ra file. I added metadata in the alpha.ra files. I added a sentace about the treatment in the .html. I updated the notes file.
  • lines changed 3, context: html, text, full: html, text
    changed references to 4Hyroxy tamoxifen to Tamoxifen at Richard's request and explained this treatment in the track dscription
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.ra
  • lines changed 458, context: html, text, full: html, text
    UW submitted another 23 files representing 13 experiments. One of those experiments had a treatment. I added treatment and fixed UW in the .daf file. I added tracks and fixed long/short labels in .ra file. I added metadata in the alpha.ra files. I added a sentace about the treatment in the .html. I updated the notes file.
  • lines changed 5, context: html, text, full: html, text
    changed references to 4Hyroxy tamoxifen to Tamoxifen at Richard's request and explained this treatment in the track dscription
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra
  • lines changed 738, context: html, text, full: html, text
    Added 7 experiments for the Jan 2011 Freeze.
  • lines changed 6, context: html, text, full: html, text
    Chagnes default visibility of all views except Signal to hide. Update windowingFunction for Signal from maximum to mean+whiskers. Downgraded max Vertical Viewing range for Signal from 30 to 20.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
  • lines changed 4217, context: html, text, full: html, text
    Added data for the Jan Freeze. Should be all of the expected data submissions.
  • lines changed 3, context: html, text, full: html, text
    Fixed typo with refrence of HUVEC cell in subTracks, that caused the data to not be displayed.
• src/hg/makeDb/trackDb/human/ntSssSnps.html
  • lines changed 4, context: html, text, full: html, text
    made mention of color colored and bold
• src/hg/makeDb/trackDb/human/trackDb.nt.ra
  • lines changed 1, context: html, text, full: html, text
    added chrom restriction to chimpDiff track
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 76, context: html, text, full: html, text
    removed troublesome alignment tracks from ucsfBrainMethyl multi-view track
• src/hg/makeDb/trackDb/human/ucsfBrainMethyl.html
  • lines changed 4, context: html, text, full: html, text
    removing references to alignments, which were taken out due to low quality. Didn't notice until Andy pointed it out when copying this track to hg19 http://redmine.soe.ucsc.edu/issues/1799
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.ra
  • lines changed 18, context: html, text, full: html, text
    Updated View Long labels to match Standars by Kate on issue #98 note 24
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 38, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added subsets of snp132: Common, Patient, Non-Unique ("Failed" for now as Paul Flicek described them)
  • lines changed 25, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added search specs for new subset tracks snp132Common, snp132Patient and snp132NonUnique.
• src/hg/makeDb/trackDb/zebrafish/danRer7/ctgPos2.html
  • lines changed 1, context: html, text, full: html, text
    Wording correction for grammar/clarity.
• src/hg/makeDb/trackDb/zebrafish/danRer7/gold.html
  • lines changed 5, context: html, text, full: html, text
    fixup two vs three groups and add links
• src/hg/pythonLib/styleGuide.txt
  • lines changed 2, context: html, text, full: html, text
    Moved Python Modules source to live under kent/python/ucscGenomics to be equivalent to java directory.
• src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
  • lines changed 122, context: html, text, full: html, text
    fixing memory-hogging 7GB
  • lines changed 84, context: html, text, full: html, text
    changed exec to fork for improved speed and reliability (9.5 minutes now instead of 11)
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    added errCatch to prevent single error from aborting the whole run
  • lines changed 109, context: html, text, full: html, text
    timeout with kill added for greater reliability
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    changed timeout to 30 seconds since at 10 seconds 3 of the jobs timed out. we may need to make this a parameter. hmm
  • lines changed 20, context: html, text, full: html, text
    fixing some of the easy memory leaks
  • lines changed 1, context: html, text, full: html, text
    incrementing the timeout some more
  • lines changed 16, context: html, text, full: html, text
    a few more leaks removed
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    Use return value from system() to avoid warning/error about ignoring it from gcc 4.4.1-4ubuntu9.
• src/inc/common.h
  • lines changed 6, context: html, text, full: html, text
    Added a couple of date routines
• src/inc/memgfx.h
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    adding section for BIGENDIAN machines
• src/lib/common.c
  • lines changed 19, context: html, text, full: html, text
    Added a couple of date routines
• src/lib/net.c
  • lines changed 2, context: html, text, full: html, text
    add FTP LIST option for directories identified by trailing slash in URL
• src/makefile
  • lines changed 4, context: html, text, full: html, text
    fix up some misunderstanding about where the gtf utilities live
• src/product/scripts/README
  • lines changed 12, context: html, text, full: html, text
    add note about the direct rsync of MySQL binary files
  • lines changed 14, context: html, text, full: html, text
    add note about hg18 split tables
• src/utils/fileExists/fileExists.c
  • lines changed 56, context: html, text, full: html, text
    initial contents
• src/utils/fileExists/makefile
  • lines changed 18, context: html, text, full: html, text
    initial contents
• src/utils/paraSync/paraSync.c
  • lines changed 47, context: html, text, full: html, text
    adding ability to recursively process FTP directories with FTP LIST output
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v246 preview2
• src/utils/sizeof/sizeof.c
  • lines changed 6, context: html, text, full: html, text
    add BIG or LITTLE endian printout message

• lines changed: 73089
• files changed: 254