All File Changes

v237_preview to v237_base (2010-07-27 to 2010-08-03) v237

• src/hg/encode/DAFs/2.0/YdhrRnaSeq.daf
  • lines changed 59, context: html, text, full: html, text
    Changed this file to be lowercase name.
• src/hg/encode/DAFs/2.0/cshlLongRnaSeq.daf
  • lines changed 3, context: html, text, full: html, text
    Checking in the most recent fiddles with these DAFs
• src/hg/encode/DAFs/2.0/haibMethylRrbs.daf
  • lines changed 17, context: html, text, full: html, text
    Checking in the most recent fiddles with these DAFs
• src/hg/encode/DAFs/2.0/licrMm9Histone.daf
  • lines changed 2, context: html, text, full: html, text
    Added nMatch and commented out revisions line
  • lines changed 4, context: html, text, full: html, text
    Updated Dafs to include updated bam validation lines, and replicates required for Peaks and Signals.
• src/hg/encode/DAFs/2.0/licrMm9Tfbs.daf
  • lines changed 2, context: html, text, full: html, text
    Added nMatch and commented out revisions line
  • lines changed 4, context: html, text, full: html, text
    Updated Dafs to include updated bam validation lines, and replicates required for Peaks and Signals.
• src/hg/encode/DAFs/2.0/psuMm95c.daf
  • lines changed 1, context: html, text, full: html, text
    Updated Hardison Grant labs bam validation (for DNA) and commented out Revision History line/
• src/hg/encode/DAFs/2.0/psuMm9DnaseSeq.daf
  • lines changed 2, context: html, text, full: html, text
    Updated Hardison Grant labs bam validation (for DNA) and commented out Revision History line/
• src/hg/encode/DAFs/2.0/psuMm9Histone.daf
  • lines changed 2, context: html, text, full: html, text
    Updated Hardison Grant labs bam validation (for DNA) and commented out Revision History line/
• src/hg/encode/DAFs/2.0/psuMm9Tfbs.daf
  • lines changed 2, context: html, text, full: html, text
    Updated Hardison Grant labs bam validation (for DNA) and commented out Revision History line/
• src/hg/encode/DAFs/2.0/ydhrRnaSeq.daf
  • lines changed 58, context: html, text, full: html, text
    Changed this file to be lowercase name.
  • lines changed 64, context: html, text, full: html, text
    Checking in the most recent fiddles with these DAFs
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 242, context: html, text, full: html, text
    first pass at modifying load scripts
• src/hg/encode/encodeLoad/doEncodeUnload.pl
  • lines changed 3, context: html, text, full: html, text
    first pass at modifying load scripts
• src/hg/encode/encodeValidate/config/cv.ra
  • lines changed 2, context: html, text, full: html, text
    Fixed two typos in terms for mouse cell lines (3143 should be 3134 and Cerebrumm should be Cerebrum).
  • lines changed 5, context: html, text, full: html, text
    Added age E0 to the age for embryonic stem cell age
  • lines changed 183, context: html, text, full: html, text
    Updated mouse registered Cell lines registered by UW lab
• src/hg/encode/encodeValidate/config/labs.ra
  • lines changed 16, context: html, text, full: html, text
    take out tim and brian
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 1, context: html, text, full: html, text
    some changes to support CSHL short transfrags
• src/hg/encode/encodeValidate/test/expected/chipseq/README.txt
  • lines changed 7, context: html, text, full: html, text
    Updated the unit test for ChipSeq. Previously was not working. Also added ability to test BAM file validation and mouse with new daf and ddf combo
• src/hg/encode/encodeValidate/test/expected/chipseq/load.ra
  • lines changed 16, context: html, text, full: html, text
    Updated the unit test for ChipSeq. Previously was not working. Also added ability to test BAM file validation and mouse with new daf and ddf combo
• src/hg/encode/encodeValidate/test/expected/chipseq/mdb.txt
  • lines changed 4, context: html, text, full: html, text
    Updated the unit test for ChipSeq. Previously was not working. Also added ability to test BAM file validation and mouse with new daf and ddf combo
• src/hg/encode/encodeValidate/test/expected/chipseq/trackDb.ra
  • lines changed 24, context: html, text, full: html, text
    Updated the unit test for ChipSeq. Previously was not working. Also added ability to test BAM file validation and mouse with new daf and ddf combo
• src/hg/encode/encodeValidate/test/input/chipseq/StanfordChip-Mouse.DAF
  • lines changed 45, context: html, text, full: html, text
    Updated the unit test for ChipSeq. Previously was not working. Also added ability to test BAM file validation and mouse with new daf and ddf combo
• src/hg/encode/encodeValidate/test/input/chipseq/StanfordChip-Test-Jun08.DDF
  • lines changed 5, context: html, text, full: html, text
    Updated the unit test for ChipSeq. Previously was not working. Also added ability to test BAM file validation and mouse with new daf and ddf combo
• src/hg/encode/encodeValidate/test/input/chipseq/StanfordChip-Test-Mouse.DDF
  • lines changed 5, context: html, text, full: html, text
    Updated the unit test for ChipSeq. Previously was not working. Also added ability to test BAM file validation and mouse with new daf and ddf combo
• src/hg/encode/encodeValidate/test/input/chipseq/StanfordChip.DAF
  • lines changed 13, context: html, text, full: html, text
    Updated the unit test for ChipSeq. Previously was not working. Also added ability to test BAM file validation and mouse with new daf and ddf combo
• src/hg/encode/encodeValidate/test/makefile
  • lines changed 1, context: html, text, full: html, text
    Updated the unit test for ChipSeq. Previously was not working. Also added ability to test BAM file validation and mouse with new daf and ddf combo
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 3, context: html, text, full: html, text
    Added line break for viewing of vendorIds
  • lines changed 52, context: html, text, full: html, text
    Changed the antibody display to accept semi-colon separated lists for the vendorName, vendorId, and orderUrl.
• src/hg/encode/validateFiles/validateFiles.c
  • lines changed 35, context: html, text, full: html, text
    add optional quality checks
  • lines changed 1, context: html, text, full: html, text
    add a verbose statement telling user what chrom is being looked at
• src/hg/hgTables/filterFields.c
  • lines changed 12, context: html, text, full: html, text
    address problem of hgTables consuming all available sockets before TIME_WAIT period by using the connection cache. Have hgTable log connection usage information to help ensure this is fixed
• src/hg/hgTables/hgTables.c
  • lines changed 6, context: html, text, full: html, text
    address problem of hgTables consuming all available sockets before TIME_WAIT period by using the connection cache. Have hgTable log connection usage information to help ensure this is fixed
• src/hg/hgTables/joining.c
  • lines changed 6, context: html, text, full: html, text
    address problem of hgTables consuming all available sockets before TIME_WAIT period by using the connection cache. Have hgTable log connection usage information to help ensure this is fixed
• src/hg/hgTables/mainPage.c
  • lines changed 2, context: html, text, full: html, text
    address problem of hgTables consuming all available sockets before TIME_WAIT period by using the connection cache. Have hgTable log connection usage information to help ensure this is fixed
• src/hg/hgTables/rangeHistogram.c
  • lines changed 4, context: html, text, full: html, text
    address problem of hgTables consuming all available sockets before TIME_WAIT period by using the connection cache. Have hgTable log connection usage information to help ensure this is fixed
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 2, context: html, text, full: html, text
    More tweeking. Make it stop.
  • lines changed 54, context: html, text, full: html, text
    Checked in Kate's navigation links, slightly modified. Feature is ifdef'd out currently
• src/hg/hgTracks/hgTracks.c
  • lines changed 17, context: html, text, full: html, text
    Finally got dragReorder row highlighting working
  • lines changed 62, context: html, text, full: html, text
    Taking some small steps towards implementing import of tracks from a data hub. Made trackDbFromRa take a url rather than a file as input by swapping in netLineFileOpen for lineFileOpen. Have a bunch of code that is compiled but not called (the call is ifdef'd out) that is starting to do some ofthe work, but that currently is crashing if ifdef'd back in. Just committing at this point so that I can do a git pull and grab everyone elses changes. I'm still learning how to work with half-baked things in git. ;-)
• src/hg/hgTracks/imageV2.c
  • lines changed 1, context: html, text, full: html, text
    Typo
  • lines changed 2, context: html, text, full: html, text
    Minor tweak to the sideButton toolTip
  • lines changed 14, context: html, text, full: html, text
    Finally got dragReorder row highlighting working
  • lines changed 21, context: html, text, full: html, text
    Slight improvements to dragReorder: toolTips and hover highlighting
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    Corrected a comment for hgIkmc track processing.
  • lines changed 8, context: html, text, full: html, text
    User John Hayward reported a sqlConnect without matching disconnect in doMiddle (genome, 6/16/10). Turns out the connection is used only in doDv() -- moved it there and converted sqlConnect to hAllocConn+hFreeConn. I don't think the dvBed track is live in any database now, so doDv is probably dead code anyway.
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 4, context: html, text, full: html, text
    adding HA RNA-seq to downloads
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 0, context: html, text, full: html, text
    fixed typo Brooke found in code review
• 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"
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 2, context: html, text, full: html, text
    adding felCat4
• src/hg/htdocs/admin/git.html
  • lines changed 89, context: html, text, full: html, text
    Updated git instructions: added links for installation and configuration, removed the gitroot directory reference, and removed instructions for customizing until we have decided what the best practice would be (or maybe this will go in genomewiki).
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 1, context: html, text, full: html, text
    Changed link to NHGRI.gif to nhgriLogo.gif, as the filename of the image was changed.
• src/hg/htdocs/goldenPath/help/blatSpec.html
  • lines changed 3, context: html, text, full: html, text
    these files were changed to use the js file that changes the url to reflect what server you are on
• src/hg/htdocs/goldenPath/help/customTrack.html
  • lines changed 2, context: html, text, full: html, text
    these files were changed to use the js file that changes the url to reflect what server you are on
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 23, context: html, text, full: html, text
    these files were changed to use the js file that changes the url to reflect what server you are on
• src/hg/htdocs/goldenPath/help/hgTablesHelp.html
  • lines changed 4, context: html, text, full: html, text
    these files were changed to use the js file that changes the url to reflect what server you are on
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 4, context: html, text, full: html, text
    these files were changed to use the js file that changes the url to reflect what server you are on
• 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 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 15, context: html, text, full: html, text
    "Release log update"
• src/hg/htdocs/images/NHGRI.gif
  • lines changed 0, context: html, text, full: html, text
    Renamed NHGRI.gif to nhgriLogo.gif because it was conflicting on filesystems that are not case-sensitive with the file nhgri.gif, also in this directory.
• src/hg/htdocs/images/nhgriLogo.gif
  • lines changed 0, context: html, text, full: html, text
    Renamed NHGRI.gif to nhgriLogo.gif because it was conflicting on filesystems that are not case-sensitive with the file nhgri.gif, also in this directory.
• src/hg/htdocs/indexIntro.html
  • lines changed 7, context: html, text, full: html, text
    Removed note about scheduled maintenance.
  • lines changed 7, context: html, text, full: html, text
    Added a temporary note about upcoming schedule maintenance.
• src/hg/htdocs/indexNews.html
  • lines changed 5, context: html, text, full: html, text
    added back edit that got stomped
• src/hg/htdocs/js/staticDoc.js
  • lines changed 12, context: html, text, full: html, text
    created a js directory for static docs, new js file that changes the url relative to the server you are on for testing purposes
• src/hg/inc/hdb.h
  • lines changed 4, context: html, text, full: html, text
    address problem of hgTables consuming all available sockets before TIME_WAIT period by using the connection cache. Have hgTable log connection usage information to help ensure this is fixed
• src/hg/inc/hui.h
  • lines changed 7, context: html, text, full: html, text
    Checked in Kate's navigation links, slightly modified. Feature is ifdef'd out currently
• src/hg/inc/jksql.h
  • lines changed 4, context: html, text, full: html, text
    address problem of hgTables consuming all available sockets before TIME_WAIT period by using the connection cache. Have hgTable log connection usage information to help ensure this is fixed
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    "New version number v237"
• src/hg/js/hgTracks.js
  • lines changed 9, context: html, text, full: html, text
    Finally got dragReorder row highlighting working
  • lines changed 25, context: html, text, full: html, text
    Slight improvements to dragReorder: toolTips and hover highlighting
• src/hg/js/hui.js
  • lines changed 1, context: html, text, full: html, text
    Minor tweek to make sure resizing doesn't obscure page border
  • lines changed 1, context: html, text, full: html, text
    Something was corrupted in this file. Hopefully it is fixed. Git???
  • lines changed 38, context: html, text, full: html, text
    Checked in Kate's navigation links, slightly modified. Feature is ifdef'd out currently
• src/hg/js/jquery.tablednd.js
  • lines changed 7, context: html, text, full: html, text
    Hopefully smoothing the dragging of tall tracks
• src/hg/js/staticDoc.js
  • lines changed 12, context: html, text, full: html, text
    moved file to be friends with the other js files
• src/hg/lib/encode/cshlShortTransfrag.as
  • lines changed 30, context: html, text, full: html, text
    cshl small rna clusters
• src/hg/lib/encode/shortFrags.as
  • lines changed 1, context: html, text, full: html, text
    changed title to match file name
  • lines changed 30, context: html, text, full: html, text
    some changes to support CSHL short transfrags
• src/hg/lib/encode/shortFrags.sql
  • lines changed 37, context: html, text, full: html, text
    some changes to support CSHL short transfrags
• src/hg/lib/hdb.c
  • lines changed 26, context: html, text, full: html, text
    address problem of hgTables consuming all available sockets before TIME_WAIT period by using the connection cache. Have hgTable log connection usage information to help ensure this is fixed
• src/hg/lib/hui.c
  • lines changed 8, context: html, text, full: html, text
    The 'top link at the top of the subtrack list needed more adjustment
  • lines changed 2, context: html, text, full: html, text
    More tweeking. Make it stop.
  • lines changed 25, context: html, text, full: html, text
    Checked in Kate's navigation links, slightly modified. Feature is ifdef'd out currently
  • lines changed 2, context: html, text, full: html, text
    Fixed missing fileName link in ... and changed tdb v. mdb metadata hint
• src/hg/lib/jksql.c
  • lines changed 19, context: html, text, full: html, text
    address problem of hgTables consuming all available sockets before TIME_WAIT period by using the connection cache. Have hgTable log connection usage information to help ensure this is fixed
• src/hg/lib/joiner.c
  • lines changed 9, context: html, text, full: html, text
    address problem of hgTables consuming all available sockets before TIME_WAIT period by using the connection cache. Have hgTable log connection usage information to help ensure this is fixed
• src/hg/lib/mdb.c
  • lines changed 7, context: html, text, full: html, text
    Fixed missing fileName link in ... and changed tdb v. mdb metadata hint
  • lines changed 3, context: html, text, full: html, text
    address problem of hgTables consuming all available sockets before TIME_WAIT period by using the connection cache. Have hgTable log connection usage information to help ensure this is fixed
• src/hg/lib/trackDbCustom.c
  • lines changed 2, context: html, text, full: html, text
    Taking some small steps towards implementing import of tracks from a data hub. Made trackDbFromRa take a url rather than a file as input by swapping in netLineFileOpen for lineFileOpen. Have a bunch of code that is compiled but not called (the call is ifdef'd out) that is starting to do some ofthe work, but that currently is crashing if ifdef'd back in. Just committing at this point so that I can do a git pull and grab everyone elses changes. I'm still learning how to work with half-baked things in git. ;-)
• src/hg/lib/useCount.sql
  • lines changed 10, context: html, text, full: html, text
    the create statement for useCount table used by useCount CGI
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    Minor tweek to make sure resizing doesn't obscure page border
  • lines changed 2, context: html, text, full: html, text
    Checked in Kate's navigation links, slightly modified. Feature is ifdef'd out currently
  • lines changed 6, context: html, text, full: html, text
    address problem of hgTables consuming all available sockets before TIME_WAIT period by using the connection cache. Have hgTable log connection usage information to help ensure this is fixed
• src/hg/makeDb/doc/calJac3.txt
  • lines changed 499, context: html, text, full: html, text
    missing self frames on multiz NwayFrames tables
• src/hg/makeDb/doc/encodeDccHg19/gencodeV4.txt
  • lines changed 3, context: html, text, full: html, text
    add 2waypseudocons
  • lines changed 45, context: html, text, full: html, text
    reload with v4fix and load Yale pseudo gene table
• src/hg/makeDb/doc/hg18.txt
  • lines changed 5, context: html, text, full: html, text
    Updated NHGRI's GWAS Catalog.
  • lines changed 49, context: html, text, full: html, text
    done with hg18 to hg19 liftOver analysis
  • lines changed 82, context: html, text, full: html, text
    trying liftOver experiments
• src/hg/makeDb/doc/hg19.txt
  • lines changed 3, context: html, text, full: html, text
    Updated NHGRI's GWAS Catalog.
  • lines changed 158, context: html, text, full: html, text
    Built genscan track for hg19.
  • lines changed 53, context: html, text, full: html, text
    trying liftOver experiments
• src/hg/makeDb/doc/mm9.txt
  • lines changed 3, context: html, text, full: html, text
    missing self frames on multiz NwayFrames tables
• src/hg/makeDb/doc/panTro2.txt
  • lines changed 36, context: html, text, full: html, text
    missing self frames on multiz NwayFrames tables
• src/hg/makeDb/doc/ponAbe2.txt
  • lines changed 37, context: html, text, full: html, text
    missing self frames on multiz NwayFrames tables
• src/hg/makeDb/schema/all.joiner
  • lines changed 3, context: html, text, full: html, text
    Removed unused identifiers (thanks Brooke).
• src/hg/makeDb/trackDb/cat/felCat4/description.html
  • lines changed 10, context: html, text, full: html, text
    changing example searches for felCat4
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 493, context: html, text, full: html, text
    add some d's onto the 1x75 sets
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeSunyalbanyRnaGeneChip.ra
  • lines changed 8, context: html, text, full: html, text
    This has the ripTgtProtien added as the antibody as well. Then It can be used either way we decide to go with the cv.ra
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/makefile
  • lines changed 6, context: html, text, full: html, text
    added 6 tracks for which we are switching to using metaDb
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeBroadChipSeq.ra
  • lines changed 11164, context: html, text, full: html, text
    adding files for tracks that we are switching to using metaDb for the metadata
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeCaltechRnaSeq.ra
  • lines changed 6759, context: html, text, full: html, text
    adding files for tracks that we are switching to using metaDb for the metadata
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeChromatinMap.ra
  • lines changed 12139, context: html, text, full: html, text
    adding files for tracks that we are switching to using metaDb for the metadata
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 1424, context: html, text, full: html, text
    staging Tim's metaDb change of inputType to controlId on hgwbeta
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeUwChIPSeq.ra
  • lines changed 12796, context: html, text, full: html, text
    adding files for tracks that we are switching to using metaDb for the metadata
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeUwDGF.ra
  • lines changed 469, context: html, text, full: html, text
    adding files for tracks that we are switching to using metaDb for the metadata
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeUwDnaseSeq.ra
  • lines changed 7608, context: html, text, full: html, text
    adding files for tracks that we are switching to using metaDb for the metadata
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeYaleChIPseq.ra
  • lines changed 2151, context: html, text, full: html, text
    staging Tim's metaDb change of inputType to controlId on hgwbeta
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/makefile
  • lines changed 6, context: html, text, full: html, text
    added 6 tracks for which we are switching to using metaDb
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeBroadChipSeq.ra
  • lines changed 11164, context: html, text, full: html, text
    adding files for tracks that we are switching to using metaDb for the metadata
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeCaltechRnaSeq.ra
  • lines changed 6759, context: html, text, full: html, text
    adding files for tracks that we are switching to using metaDb for the metadata
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeChromatinMap.ra
  • lines changed 12139, context: html, text, full: html, text
    adding files for tracks that we are switching to using metaDb for the metadata
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 1424, context: html, text, full: html, text
    prepping to release Tim's metaDb change of inputType to controlId
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeUwChIPSeq.ra
  • lines changed 12796, context: html, text, full: html, text
    adding files for tracks that we are switching to using metaDb for the metadata
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeUwDGF.ra
  • lines changed 469, context: html, text, full: html, text
    adding files for tracks that we are switching to using metaDb for the metadata
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeUwDnaseSeq.ra
  • lines changed 7608, context: html, text, full: html, text
    adding files for tracks that we are switching to using metaDb for the metadata
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeYaleChIPseq.ra
  • lines changed 2151, context: html, text, full: html, text
    prepping to release Tim's metaDb change of inputType to controlId
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 20, context: html, text, full: html, text
    set Brain Methyl to show mismatches, discover all the alignments are off by one
  • lines changed 0, context: html, text, full: html, text
    take out some spaces in Brain Methyl short labels (per Mary)
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 35, context: html, text, full: html, text
    standardized longLabels (super, track & subtrack) for ENCODE Regulation track; made one fix, changed 8 to 9 in one track longLabel; removed confusing parentheses from another track longLabel
  • lines changed 13, context: html, text, full: html, text
    made Encode Regulation track first in Regulation group; enabled subTrack drag/reorder
  • lines changed 107, context: html, text, full: html, text
    Making little logo show up to left of encode regulatory track and fixing long label on one component.
  • lines changed 2, context: html, text, full: html, text
    incorporating changes to the short and long labels for yale rna-seq track
  • lines changed 5, context: html, text, full: html, text
    changing *.new.ra to .ra for 5 tracks for which we are switching to using the metaDb table, techincally already on RR, since release tags weren't used
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncodeYaleRnaSeq.new.ra
  • lines changed 7, context: html, text, full: html, text
    incorporating changes to the short and long labels for yale rna-seq track
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncodeYaleRnaSeq.ra
  • lines changed 20, context: html, text, full: html, text
    incorporating changes to the short and long labels for yale rna-seq track
• src/hg/makeDb/trackDb/human/hg18/ucsfBrainMethyl.html
  • lines changed 1, context: html, text, full: html, text
    changing description of how alignments are colored
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.ra
  • lines changed 177, context: html, text, full: html, text
    copied the *.new.ra over the .ra; would normally be prep for release, but trackDb.wgEncode.ra had include lines for the *new.ra without any release tags, so already on rr
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.new.ra
  • lines changed 140, context: html, text, full: html, text
    copying *.ra over *.new.ra because Brian accidentally made the changes to *.ra instead of *.new.ra; getting *.ra & *.new.ra are back in sync as they should be when releasing new changes (even though this was accidentally already released because release tags weren't used
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.ra
  • lines changed 234, context: html, text, full: html, text
    copied the *.new.ra over the .ra; would normally be prep for release, but trackDb.wgEncode.ra had include lines for the *new.ra without any release tags, so already on rr
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaRnaSeq.html
  • lines changed 2, context: html, text, full: html, text
    changing RPKM description
  • lines changed 1, context: html, text, full: html, text
    fixing up description page
  • lines changed 5, context: html, text, full: html, text
    adding some info to the description
• src/hg/makeDb/trackDb/human/hg18/wgEncodeReg.html
  • lines changed 7, context: html, text, full: html, text
    fixed the wording on the descriptions for the regulatory track on hg18
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegMarkEnhH3k27ac.html
  • lines changed 8, context: html, text, full: html, text
    added ENCODE Data Release policy
  • lines changed 8, context: html, text, full: html, text
    fixed the wording on the descriptions for the regulatory track on hg18
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegMarkEnhH3k4me1.html
  • lines changed 8, context: html, text, full: html, text
    added ENCODE Data Release policy
  • lines changed 8, context: html, text, full: html, text
    fixed the wording on the descriptions for the regulatory track on hg18
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegMarkEnhH3k4me3.html
  • lines changed 8, context: html, text, full: html, text
    added ENCODE Data Release policy
  • lines changed 8, context: html, text, full: html, text
    fixed the wording on the descriptions for the regulatory track on hg18
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegTfbsClustered.html
  • lines changed 4, context: html, text, full: html, text
    made some edits to the first sentence of description to improve clarity
  • lines changed 1, context: html, text, full: html, text
    rechecking this in with the new link
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegTxn.html
  • lines changed 8, context: html, text, full: html, text
    added ENCODE Data Release policy
  • lines changed 7, context: html, text, full: html, text
    fixed the wording on the descriptions for the regulatory track on hg18
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwChIPSeq.ra
  • lines changed 340, context: html, text, full: html, text
    copied the *.new.ra over the .ra; would normally be prep for release, but trackDb.wgEncode.ra had include lines for the *new.ra without any release tags, so already on rr
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDGF.ra
  • lines changed 20, context: html, text, full: html, text
    copied the *.new.ra over the .ra; would normally be prep for release, but trackDb.wgEncode.ra had include lines for the *new.ra without any release tags, so already on rr
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.ra
  • lines changed 234, context: html, text, full: html, text
    copied the *.new.ra over the .ra; would normally be prep for release, but trackDb.wgEncode.ra had include lines for the *new.ra without any release tags, so already on rr
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 176, context: html, text, full: html, text
    added origAssembly and corrected dates
  • lines changed 1758, context: html, text, full: html, text
    Revert "These files have all had origAssembly added, but they will need to have the release date modified"The CshlShort had affy informaiton in it. I need to start this over. This reverts commit 196e751a37514efca4687d4d0e50fb4ca8e71a8e. Conflicts: src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra
  • lines changed 1759, context: html, text, full: html, text
    These files have all had origAssembly added, but they will need to have the release date modified
  • lines changed 221, context: html, text, full: html, text
    add transfrags
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra
  • lines changed 31, context: html, text, full: html, text
    add origAssembly, and get submission and restriction end dates from hg18
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra
  • lines changed 57, context: html, text, full: html, text
    The correct magic number
  • lines changed 18, context: html, text, full: html, text
    The meta data is changed to reflect the orig assembly and the correct dates.
  • lines changed 21, context: html, text, full: html, text
    Revert "These files have all had origAssembly added, but they will need to have the release date modified"The CshlShort had affy informaiton in it. I need to start this over. This reverts commit 196e751a37514efca4687d4d0e50fb4ca8e71a8e. Conflicts: src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra
  • lines changed 18, context: html, text, full: html, text
    Changed the metadata and the short labels for GisRnaSeq
  • lines changed 33, context: html, text, full: html, text
    These files have all had origAssembly added, but they will need to have the release date modified
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 1176, context: html, text, full: html, text
    Updated Track matrix and metadata
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 137, context: html, text, full: html, text
    Revert "These files have all had origAssembly added, but they will need to have the release date modified"The CshlShort had affy informaiton in it. I need to start this over. This reverts commit 196e751a37514efca4687d4d0e50fb4ca8e71a8e. Conflicts: src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra
  • lines changed 137, context: html, text, full: html, text
    These files have all had origAssembly added, but they will need to have the release date modified
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyTiling.ra
  • lines changed 9, context: html, text, full: html, text
    This commit really has the metaDb changes for SunyAlbanyTiling. With the addition of antibody as well as ripTgtProtien.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyGeneST.ra
  • lines changed 22, context: html, text, full: html, text
    This is the metadata for Suny updated with the antibody, the ripTgtProtien has not been removed
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyTiling.ra
  • lines changed 145, context: html, text, full: html, text
    File made on accident
  • lines changed 145, context: html, text, full: html, text
    This is the metadata for Suny updated with the antibody, the ripTgtProtien has not been removed
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 753, context: html, text, full: html, text
    Added 7 new submissions. Still prelimary display, needs clean up.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 377, context: html, text, full: html, text
    Added 4 new submissions. 2087-2090
  • lines changed 191, context: html, text, full: html, text
    Removed all metadata for 2 submission: 2041,2042 as advised from lab
  • lines changed 3723, context: html, text, full: html, text
    Added 38 new submissions. Updated short labels to be consistent with previous data.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 951, context: html, text, full: html, text
    Add 8 new submissions and accompanying metaData for UW Histone Track
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 7, context: html, text, full: html, text
    add 2waypseudocons to gencode track
  • lines changed 2, context: html, text, full: html, text
    add yale pseudoGene track for gencode v4
  • lines changed 2, context: html, text, full: html, text
    I have changed the names of the include files to match the standard. I also have been working on the short labels for the Suny tracks.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeHaibRrbs.ra
  • lines changed 1, context: html, text, full: html, text
    Updated Methyl Data to be in one composite
  • lines changed 2, context: html, text, full: html, text
    Updated Track matrix and metadata
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeSuny.ra
  • lines changed 246, context: html, text, full: html, text
    I have changed the names of the include files to match the standard. I also have been working on the short labels for the Suny tracks.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeSunyAlbanyTiling.ra
  • lines changed 111, context: html, text, full: html, text
    I have changed the names of the include files to match the standard. I also have been working on the short labels for the Suny tracks.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeSydhTfbs.ra
  • lines changed 14, context: html, text, full: html, text
    Added Notes section to provide information on track specifications
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.html
  • lines changed 106, context: html, text, full: html, text
    copy over from hg18
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.ra
  • lines changed 121, context: html, text, full: html, text
    add transfrags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencode.html
  • lines changed 25, context: html, text, full: html, text
    changes from Felix
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.html
  • lines changed 15, context: html, text, full: html, text
    Added the methods changes from Atif Shahab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.ra
  • lines changed 72, context: html, text, full: html, text
    set BAM options to show mismatches etc
  • lines changed 18, context: html, text, full: html, text
    fix labels and defaults
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.html
  • lines changed 3, context: html, text, full: html, text
    removed the reference to all raw signal
  • lines changed 3, context: html, text, full: html, text
    removed the reference to split alignments
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra
  • lines changed 46, context: html, text, full: html, text
    Changed the metadata and the short labels for GisRnaSeq
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl27.ra
  • lines changed 1, context: html, text, full: html, text
    Updated Methyl Data to be in one composite
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Updated Methyl Data to be in one composite
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra
  • lines changed 3, context: html, text, full: html, text
    Updated Short and long lables to be consistent with the TFBS tracks. Moved data from Dnase supertrack to TFBS supertrack
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 0, context: html, text, full: html, text
    added a space
  • lines changed 31, context: html, text, full: html, text
    Changed the long and short labels to include antibody
  • lines changed 4, context: html, text, full: html, text
    Changed the antibody from upper case to lower case.
  • lines changed 246, context: html, text, full: html, text
    I have changed the names of the include files to match the standard. I also have been working on the short labels for the Suny tracks.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.ra
  • lines changed 1, context: html, text, full: html, text
    Changed the antibody from upper case to lower case.
  • lines changed 111, context: html, text, full: html, text
    I have changed the names of the include files to match the standard. I also have been working on the short labels for the Suny tracks.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.html
  • lines changed 9, context: html, text, full: html, text
    Updated each track description with feedback provided by the UW lab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra
  • lines changed 282, context: html, text, full: html, text
    Added 7 new submissions. Still prelimary display, needs clean up.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.html
  • lines changed 15, context: html, text, full: html, text
    Updated each track description with feedback provided by the UW lab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
  • lines changed 121, context: html, text, full: html, text
    Added 4 new submissions. 2087-2090
  • lines changed 60, context: html, text, full: html, text
    Removed submission 2041 and 2042 as advised by the lab
  • lines changed 1153, context: html, text, full: html, text
    Added 38 new submissions. Updated short labels to be consistent with previous data.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.html
  • lines changed 13, context: html, text, full: html, text
    Updated each track description with feedback provided by the UW lab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra
  • lines changed 224, context: html, text, full: html, text
    Add 8 new submissions and accompanying metaData for UW Histone Track
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    missing self frames on multiz NwayFrames tables
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 717, context: html, text, full: html, text
    Split up Stan/Yale TFBS data and Histone data into own trackDb's. Update encode trackDb to have only include statements of the encode composites
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncodeSydhHist.ra
  • lines changed 145, context: html, text, full: html, text
    Split up Stan/Yale TFBS data and Histone data into own trackDb's. Update encode trackDb to have only include statements of the encode composites
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncodeSydhTfbs.ra
  • lines changed 571, context: html, text, full: html, text
    Split up Stan/Yale TFBS data and Histone data into own trackDb's. Update encode trackDb to have only include statements of the encode composites
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 51, context: html, text, full: html, text
    adding felCat4 chain/net track
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    do not need to have useCount on the list of browser bins, make it when desired, it is a one-off
  • lines changed 1, context: html, text, full: html, text
    adding useCount to BROWSER_BINS
• src/hg/near/hgNear/go.c
  • lines changed 18, context: html, text, full: html, text
    handling uniProt connection properly for hgNear GO column so we do not use up thousands of connections unnecessarily
• src/hg/near/hgNear/hgNear.h
  • lines changed 1, context: html, text, full: html, text
    handling uniProt connection properly for hgNear GO column so we do not use up thousands of connections unnecessarily
• src/hg/near/hgNear/hgNearData/S_cerevisiae/columnDb.ra
  • lines changed 3, context: html, text, full: html, text
    Reverse the selfBlastTab table name change.
  • lines changed 3, context: html, text, full: html, text
    Update the selfBlastTab table name.
• src/hg/near/hgNear/hgNearData/S_cerevisiae/orderDb.ra
  • lines changed 1, context: html, text, full: html, text
    Reverse the selfBlastTab table name change.
  • lines changed 1, context: html, text, full: html, text
    Update the selfBlastTab table name.
• src/hg/useCount/makefile
  • lines changed 16, context: html, text, full: html, text
    initial contents for useCount
• src/hg/useCount/useCount.c
  • lines changed 62, context: html, text, full: html, text
    initial contents for useCount
• src/hg/utils/automation/Encode.pm
  • lines changed 1, context: html, text, full: html, text
    some changes to support CSHL short transfrags
• src/hg/utils/makefile
  • lines changed 2, context: html, text, full: html, text
    add gffToPsl
• src/inc/cheapcgi.h
  • lines changed 24, context: html, text, full: html, text
    Added cgiClientBrowser() routine to determine browser from HTTP_USER_AGENT
• src/inc/memgfx.h
  • lines changed 3, context: html, text, full: html, text
    add transparency for 32-bit PNG. Tim needs it for drag scroll
• src/lib/cheapcgi.c
  • lines changed 7, context: html, text, full: html, text
    Minor adjustments to client resolution code
  • lines changed 94, context: html, text, full: html, text
    Added cgiClientBrowser() routine to determine browser from HTTP_USER_AGENT
• src/lib/common.c
  • lines changed 1, context: html, text, full: html, text
    Minor fix to skipBeyondDelimit
• src/lib/errabort.c
  • lines changed 12, context: html, text, full: html, text
    Hiram noticed this code broke cygwin build, so I ifdef'd it out. It is a rarely handy tool to peak at the stack in a cgi without aborting
• src/lib/htmshell.c
  • lines changed 4, context: html, text, full: html, text
    htmlEncode has been imprived with a newline char. However, FF does not support it
• src/lib/memgfx.c
  • lines changed 13, context: html, text, full: html, text
    add transparency for 32-bit PNG. Tim needs it for drag scroll
• src/lib/mgCircle.c
  • lines changed 0, context: html, text, full: html, text
    fixing perms on mgCircle.c
• src/lib/vPng.c
  • lines changed 3, context: html, text, full: html, text
    add transparency for 32-bit PNG. Tim needs it for drag scroll
• src/product/README.local.git.source
  • lines changed 59, context: html, text, full: html, text
    Updated git instructions: added links for installation and configuration, removed the gitroot directory reference, and removed instructions for customizing until we have decided what the best practice would be (or maybe this will go in genomewiki).
• src/utils/htmlCheck/htmlCheck.c
  • lines changed 0, context: html, text, full: html, text
    Fixed indentation.
• src/utils/qa/checkGenomeMysql
  • lines changed 65, context: html, text, full: html, text
    adding script to check functionality of genome-mysql
• src/utils/qa/makefile
  • lines changed 1, context: html, text, full: html, text
    adding checkGenomeMysql to the makefile
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v237 final build

• lines changed: 130382
• files changed: 257