All File Changes

v240_preview to v240_base (2010-09-07 to 2010-09-14) v240

• src/ameme/makefile
  • lines changed 1, context: html, text, full: html, text
    fixup build on cygwin
• src/hg/cartDump/cartDump.c
  • lines changed 13, context: html, text, full: html, text
    hgTrackUi can now use ajax to update composite/view settings, which enables keeping subtrack level v. composite/view level settings properly influencing each other. That is, timing is important in ensuring that composite/view level changes overrides subtrack level settings. The triggers for this code in hui.c are all ifdef'd on SUBTRACK_CFG_POPUP.
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • lines changed 1, context: html, text, full: html, text
    Fix a typo found by Jim
• src/hg/encode/encodeValidate/config/cv.ra
  • lines changed 2, context: html, text, full: html, text
    Updated Tier information for H1-hESC and NHEK cell lines. Upgraded H1-hESC to tier 1 and downgraded NHEK to tier 3
  • lines changed 34, context: html, text, full: html, text
    Updated validation document nameing, so that links to documents would work. Also sperated two antibodies for target YY1
  • lines changed 49, context: html, text, full: html, text
    Added 4 new antibody validation document refrences and 3 new antibodies (BCLAF1(M33-P5B11), ATF3, GATA-2(CG2-96) and LEF-1(C-19)) for the Myers lab.
  • lines changed 7, context: html, text, full: html, text
    Updated registration term names for GATA2_(CG2-96) and LEF1_(C-19) to be consistent with ncbi naming of the genes. Also updated antibody document link to specify Myers lab for ATF3 antibody
  • lines changed 1, context: html, text, full: html, text
    Shortened tag for BoneMarrow to BMarrow to fit table name of 64 characters.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 14, context: html, text, full: html, text
    Added tdbLimitedByAncestry() and used it to fix 2 vis problems: cfg popup and findTracks initial vis
• src/hg/hgTracks/bamTrack.c
  • lines changed 1, context: html, text, full: html, text
    Support conditional center labels for dense subtracks in both C and JS. Top dense subtrack in a set will show centerLabel of composite.
• src/hg/hgTracks/config.c
  • lines changed 18, context: html, text, full: html, text
    Cleaned up a lot of obsolete ifdefs, now that dragReorder and flatTracks are on the RR
• src/hg/hgTracks/expRatioTracks.c
  • lines changed 1, context: html, text, full: html, text
    Support conditional center labels for dense subtracks in both C and JS. Top dense subtrack in a set will show centerLabel of composite.
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    Put blueBar on a diet. Really we need css and bluBar as lib function.
  • lines changed 1, context: html, text, full: html, text
    blue lines were off on bg image
  • lines changed 176, context: html, text, full: html, text
    Cleaned up a lot of obsolete ifdefs, now that dragReorder and flatTracks are on the RR
  • lines changed 29, context: html, text, full: html, text
    Support conditional center labels for dense subtracks in both C and JS. Top dense subtrack in a set will show centerLabel of composite.
  • lines changed 2, context: html, text, full: html, text
    Right click view image must use regen a non-imageV2 image, due to conditional centerLabels in imageV2, among other things.
• src/hg/hgTracks/hgTracks.h
  • lines changed 9, context: html, text, full: html, text
    Cleaned up a lot of obsolete ifdefs, now that dragReorder and flatTracks are on the RR
  • lines changed 12, context: html, text, full: html, text
    Support conditional center labels for dense subtracks in both C and JS. Top dense subtrack in a set will show centerLabel of composite.
• src/hg/hgTracks/imageV2.c
  • lines changed 26, context: html, text, full: html, text
    Cleaned up a lot of obsolete ifdefs, now that dragReorder and flatTracks are on the RR
  • lines changed 2, context: html, text, full: html, text
    Subtrack wigs can be packed.
  • lines changed 3, context: html, text, full: html, text
    Further sorting out the difference between canPack and shouldPack
  • lines changed 88, context: html, text, full: html, text
    Support conditional center labels for dense subtracks in both C and JS. Top dense subtrack in a set will show centerLabel of composite.
• src/hg/hgTracks/imageV2.h
  • lines changed 83, context: html, text, full: html, text
    Cleaned up a lot of obsolete ifdefs, now that dragReorder and flatTracks are on the RR
  • lines changed 19, context: html, text, full: html, text
    Support conditional center labels for dense subtracks in both C and JS. Top dense subtrack in a set will show centerLabel of composite.
• src/hg/hgTracks/mainMain.c
  • lines changed 1, context: html, text, full: html, text
    Right click view image must use regen a non-imageV2 image, due to conditional centerLabels in imageV2, among other things.
• src/hg/hgTracks/searchTracks.c
  • lines changed 14, context: html, text, full: html, text
    Added tdbLimitedByAncestry() and used it to fix 2 vis problems: cfg popup and findTracks initial vis
  • lines changed 24, context: html, text, full: html, text
    Further sorting out the difference between canPack and shouldPack
  • lines changed 15, context: html, text, full: html, text
    Extended white list of mdb vars and changed some labelling.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 5, context: html, text, full: html, text
    Cleaned up a lot of obsolete ifdefs, now that dragReorder and flatTracks are on the RR
  • lines changed 14, context: html, text, full: html, text
    Support conditional center labels for dense subtracks in both C and JS. Top dense subtrack in a set will show centerLabel of composite.
  • lines changed 2, context: html, text, full: html, text
    Fixed bug where found and selected tracks were not displayed in browser because the '_sel' setting was being removed as redundant.
• src/hg/hgTracks/wigTrack.c
  • lines changed 3, context: html, text, full: html, text
    Cleaned up a lot of obsolete ifdefs, now that dragReorder and flatTracks are on the RR
  • lines changed 1, context: html, text, full: html, text
    fix overflow bug problem double value becoming int value
• src/hg/hgc/hgc.c
  • lines changed 49, context: html, text, full: html, text
    finidh up NumTs
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 15, context: html, text, full: html, text
    Added new hg19 section and the GIS DNA PET track that was just released
  • lines changed 1, context: html, text, full: html, text
    fixed typo
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 432, context: html, text, full: html, text
    Massive update of contributors section
  • lines changed 18, context: html, text, full: html, text
    Added a few more items from Bob.
• src/hg/htdocs/goldenPath/help/bigWig.html
  • lines changed 1, context: html, text, full: html, text
    fixing path, file got moved down a level
• src/hg/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    Added tdbLimitedByAncestry() and used it to fix 2 vis problems: cfg popup and findTracks initial vis
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v240
• src/hg/js/ajax.js
  • lines changed 103, context: html, text, full: html, text
    Tangled code that allows form submits to wait for outstanding ajax completion.
  • lines changed 3, context: html, text, full: html, text
    Added support for setCartVars to trigger compositeTdbCleanupOverrides... that is ajax can now trigger the handling of subtrack v. composite/view setting overrides
• src/hg/js/hgTracks.js
  • lines changed 5, context: html, text, full: html, text
    fix problem in safari when groups are hidden
  • lines changed 1, context: html, text, full: html, text
    set font-family for tabs div to fix problem where it was getting set to Arial (I think via jquery-ui.css)
  • lines changed 2, context: html, text, full: html, text
    Added tdbLimitedByAncestry() and used it to fix 2 vis problems: cfg popup and findTracks initial vis
  • lines changed 8, context: html, text, full: html, text
    Further sorting out the difference between canPack and shouldPack
  • lines changed 48, context: html, text, full: html, text
    Support conditional center labels for dense subtracks in both C and JS. Top dense subtrack in a set will show centerLabel of composite.
  • lines changed 7, context: html, text, full: html, text
    Right click view image must use regen a non-imageV2 image, due to conditional centerLabels in imageV2, among other things.
  • lines changed 33, context: html, text, full: html, text
    Fixed bug where found and selected tracks were not displayed in browser because the '_sel' setting was being removed as redundant.
• src/hg/js/hui.js
  • lines changed 21, context: html, text, full: html, text
    hgTrackUi can now use ajax to update composite/view settings, which enables keeping subtrack level v. composite/view level settings properly influencing each other. That is, timing is important in ensuring that composite/view level changes overrides subtrack level settings. The triggers for this code in hui.c are all ifdef'd on SUBTRACK_CFG_POPUP.
  • lines changed 1, context: html, text, full: html, text
    Removed 'FIXME' which has been fixed.
• src/hg/js/utils.js
  • lines changed 18, context: html, text, full: html, text
    Added support for setCartVars to trigger compositeTdbCleanupOverrides... that is ajax can now trigger the handling of subtrack v. composite/view setting overrides
• src/hg/lib/cart.c
  • lines changed 61, context: html, text, full: html, text
    hgTrackUi can now use ajax to update composite/view settings, which enables keeping subtrack level v. composite/view level settings properly influencing each other. That is, timing is important in ensuring that composite/view level changes overrides subtrack level settings. The triggers for this code in hui.c are all ifdef'd on SUBTRACK_CFG_POPUP.
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    fix incorrect use of printf detect by gcc 4.4.3
  • lines changed 98, context: html, text, full: html, text
    hgTrackUi can now use ajax to update composite/view settings, which enables keeping subtrack level v. composite/view level settings properly influencing each other. That is, timing is important in ensuring that composite/view level changes overrides subtrack level settings. The triggers for this code in hui.c are all ifdef'd on SUBTRACK_CFG_POPUP.
  • lines changed 6, context: html, text, full: html, text
    Removed a TODO list which has been done.
  • lines changed 22, context: html, text, full: html, text
    Added tdbLimitedByAncestry() and used it to fix 2 vis problems: cfg popup and findTracks initial vis
• src/hg/lib/liftOver.c
  • lines changed 4, context: html, text, full: html, text
    improving liftOver -errorHelp message
• src/hg/lib/wigDataStream.c
  • lines changed 1, context: html, text, full: html, text
    removing old constraint for custom track file business
• src/hg/makeDb/doc/ce9.txt
  • lines changed 124, context: html, text, full: html, text
    genbank running and started sangerGene
  • lines changed 458, context: html, text, full: html, text
    genbank done and working on sangerGene and gene sorter installation
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added ce9 - C. elegans WS210
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added ce9 - C. elegans WS210
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    adding darned table for hg
• src/hg/makeDb/trackDb/README
  • lines changed 1, context: html, text, full: html, text
    added info about what happens if no priority line is included for a track
  • lines changed 1, context: html, text, full: html, text
    Added priority default is 100
• src/hg/makeDb/trackDb/human/agilentCgh.html
  • lines changed 150, context: html, text, full: html, text
    trackDbs were split into different stanzas for release status, but they had different parent track names. Now they are the same, and the subTracks are referencing the correct parent name as well. Renamed old HTML description to match.
  • lines changed 19, context: html, text, full: html, text
    got rid of the two CNV arrays from the public/beta description
• src/hg/makeDb/trackDb/human/agilentCgh.notPublic.html
  • lines changed 123, context: html, text, full: html, text
    hg18 tracks were bed 6 and hg19 are bed 4. Unlike the rat and mouse tracks, they are all the same type in each assembly at least, so the noInherit-on stuff is not necessary. For the beta/public track, it's bed 6. this is quite complicated.
• src/hg/makeDb/trackDb/human/agilentCghAlpha.html
  • lines changed 123, context: html, text, full: html, text
    hg18 tracks were bed 6 and hg19 are bed 4. Unlike the rat and mouse tracks, they are all the same type in each assembly at least, so the noInherit-on stuff is not necessary. For the beta/public track, it's bed 6. this is quite complicated.
• src/hg/makeDb/trackDb/human/agilentProbes.html
  • lines changed 150, context: html, text, full: html, text
    trackDbs were split into different stanzas for release status, but they had different parent track names. Now they are the same, and the subTracks are referencing the correct parent name as well. Renamed old HTML description to match.
• src/hg/makeDb/trackDb/human/darned.html
  • lines changed 1, context: html, text, full: html, text
    adding in missing period in the references
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    finish NumtS
  • lines changed 3, context: html, text, full: html, text
    hg18 tracks were bed 6 and hg19 are bed 4. Unlike the rat and mouse tracks, they are all the same type in each assembly at least, so the noInherit-on stuff is not necessary. For the beta/public track, it's bed 6. this is quite complicated.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    removing ENCODE GIS DNA PET priority so that it defaults to 100 and will sort after the SNP(#) tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGencode.ra
  • lines changed 5, context: html, text, full: html, text
    copied alpha version to beta since Brian had made some corrections
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 2, context: html, text, full: html, text
    getting ready to release the meta data for GisDnaPet
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.ra
  • lines changed 1, context: html, text, full: html, text
    Updated Tier information for H1-hESC and NHEK cell lines. Upgraded H1-hESC to tier 1 and downgraded NHEK to tier 3
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Updated Tier information for H1-hESC and NHEK cell lines. Upgraded H1-hESC to tier 1 and downgraded NHEK to tier 3
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.ra
  • lines changed 1, context: html, text, full: html, text
    removed the Priority so that the track would not be the first track in that group
  • lines changed 6, context: html, text, full: html, text
    removed release tags in preparation for the release of the GIS DNA PET track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Updated Tier information for H1-hESC and NHEK cell lines. Upgraded H1-hESC to tier 1 and downgraded NHEK to tier 3
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 1, context: html, text, full: html, text
    Updated Tier information for H1-hESC and NHEK cell lines. Upgraded H1-hESC to tier 1 and downgraded NHEK to tier 3
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra
  • lines changed 1, context: html, text, full: html, text
    Updated Tier information for H1-hESC and NHEK cell lines. Upgraded H1-hESC to tier 1 and downgraded NHEK to tier 3
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra
  • lines changed 1, context: html, text, full: html, text
    Updated Tier information for H1-hESC and NHEK cell lines. Upgraded H1-hESC to tier 1 and downgraded NHEK to tier 3
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra
  • lines changed 1, context: html, text, full: html, text
    Updated Tier information for H1-hESC and NHEK cell lines. Upgraded H1-hESC to tier 1 and downgraded NHEK to tier 3
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRnaSeqSuper.html
  • lines changed 4, context: html, text, full: html, text
    fixed misspelling of occurence
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 1, context: html, text, full: html, text
    Updated Tier information for H1-hESC and NHEK cell lines. Upgraded H1-hESC to tier 1 and downgraded NHEK to tier 3
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
  • lines changed 8, context: html, text, full: html, text
    Updated Tier information for H1-hESC and NHEK cell lines. Upgraded H1-hESC to tier 1 and downgraded NHEK to tier 3
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra
  • lines changed 1, context: html, text, full: html, text
    Updated Tier information for H1-hESC and NHEK cell lines. Upgraded H1-hESC to tier 1 and downgraded NHEK to tier 3
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 17, context: html, text, full: html, text
    trackDbs were split into different stanzas for release status, but they had different parent track names. Now they are the same, and the subTracks are referencing the correct parent name as well. Renamed old HTML description to match.
  • lines changed 6, context: html, text, full: html, text
    hg18 tracks were bed 6 and hg19 are bed 4. Unlike the rat and mouse tracks, they are all the same type in each assembly at least, so the noInherit-on stuff is not necessary. For the beta/public track, it's bed 6. this is quite complicated.
• src/hg/makeDb/trackDb/marmoset/calJac3/multiz13way.html
  • lines changed 364, context: html, text, full: html, text
    13-way description
  • lines changed 4, context: html, text, full: html, text
    polishing multiz13way.html
  • lines changed 7, context: html, text, full: html, text
    touch up html
• src/hg/makeDb/trackDb/marmoset/calJac3/phastConsElements13way.html
  • lines changed 96, context: html, text, full: html, text
    13-way description
• src/hg/makeDb/trackDb/mouse/agilentCgh.notPublic.html
  • lines changed 90, context: html, text, full: html, text
    changed name of the alpha version of the html
• src/hg/makeDb/trackDb/mouse/agilentCghAlpha.html
  • lines changed 90, context: html, text, full: html, text
    changed name of the alpha version of the html
• src/hg/makeDb/trackDb/mouse/agilentCghBeta.html
  • lines changed 57, context: html, text, full: html, text
    Removed a track from beta and separated out public, which still has the track.
  • lines changed 2, context: html, text, full: html, text
    pushing out changes on beta to the rr for agilent track
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    changed name of the alpha version of the html
  • lines changed 25, context: html, text, full: html, text
    New tables were bed 4 instead of bed 6, so the noInherit-on composite track needed to be on
  • lines changed 41, context: html, text, full: html, text
    Removed a track from beta and separated out public, which still has the track.
  • lines changed 40, context: html, text, full: html, text
    pushing out changes on beta to the rr for agilent track
• src/hg/makeDb/trackDb/rat/agilentCgh.html
  • lines changed 2, context: html, text, full: html, text
    pushing out changes on beta to the rr for agilent track
• src/hg/makeDb/trackDb/rat/agilentCgh.notPublic.html
  • lines changed 90, context: html, text, full: html, text
    New tables were bed 4 instead of bed 6, so the noInherit-on composite track needed to be on
• src/hg/makeDb/trackDb/rat/agilentCghAlpha.html
  • lines changed 90, context: html, text, full: html, text
    New tables were bed 4 instead of bed 6, so the noInherit-on composite track needed to be on
• src/hg/makeDb/trackDb/rat/trackDb.ra
  • lines changed 25, context: html, text, full: html, text
    New tables were bed 4 instead of bed 6, so the noInherit-on composite track needed to be on
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    Adding 'intronGap 12' to knownGene at Jim's request. Related to Redmine #954.
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Adding 'intronGap 12' to knownGene at Jim's request. Related to Redmine #954.
  • lines changed 7, context: html, text, full: html, text
    lowering priority of SNP(#) tracks so they are lower than the default 100 priority
• src/hg/makeDb/trackDb/worm/ce9/sangerGene.html
  • lines changed 16, context: html, text, full: html, text
    adding sangerGene track
• src/hg/makeDb/trackDb/worm/ce9/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    adding sangerGene track
• src/hg/mouseStuff/bedCoverage/bedCoverage.c
  • lines changed 2, context: html, text, full: html, text
    fixed C99 incompatiblities
• src/hg/mouseStuff/mafCoverage/mafCoverage.c
  • lines changed 2, context: html, text, full: html, text
    fixed C99 incompatiblities
• src/hg/utils/gtfToGenePred/gtfToGenePred.c
  • lines changed 188, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/hg/utils/gtfToGenePred/makefile
  • lines changed 21, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/hg/utils/gtfToGenePred/tests/expected/basic.gp
  • lines changed 4, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/hg/utils/gtfToGenePred/tests/expected/basic.info
  • lines changed 5, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/hg/utils/gtfToGenePred/tests/expected/dups.gp
  • lines changed 2, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/hg/utils/gtfToGenePred/tests/expected/dups.out
  • lines changed 3, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/hg/utils/gtfToGenePred/tests/expected/ensembl.gp
  • lines changed 2, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/hg/utils/gtfToGenePred/tests/expected/ensembl.info
  • lines changed 3, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/hg/utils/gtfToGenePred/tests/expected/geneNameAsName2.gp
  • lines changed 2, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/hg/utils/gtfToGenePred/tests/expected/impliedStop.gp
  • lines changed 6, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/hg/utils/gtfToGenePred/tests/expected/impliedStop.info
  • lines changed 7, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/hg/utils/gtfToGenePred/tests/expected/splitStop.gp
  • lines changed 2, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/hg/utils/gtfToGenePred/tests/expected/srcPre.gp
  • lines changed 3, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/hg/utils/gtfToGenePred/tests/expected/srcPre.info
  • lines changed 4, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/hg/utils/gtfToGenePred/tests/input/basic.gtf
  • lines changed 14, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/hg/utils/gtfToGenePred/tests/input/dups.gtf
  • lines changed 19, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/hg/utils/gtfToGenePred/tests/input/ensembl.gtf
  • lines changed 12, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/hg/utils/gtfToGenePred/tests/input/flybase.gtf
  • lines changed 56, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/hg/utils/gtfToGenePred/tests/input/split.gtf
  • lines changed 5, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/hg/utils/gtfToGenePred/tests/input/splitStop.gtf
  • lines changed 34, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/hg/utils/gtfToGenePred/tests/makefile
  • lines changed 56, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
  • lines changed 1, context: html, text, full: html, text
    fixed make error caused by directory move
• src/hg/utils/makefile
  • lines changed 2, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/hg/utils/refSeqGet/refSeqVerInfo.c
  • lines changed 4, context: html, text, full: html, text
    fixed C99 incompatiblities
• src/inc/common.mk
  • lines changed 1, context: html, text, full: html, text
    fixup build on cygwin
• src/lib/pipeline.c
  • lines changed 4, context: html, text, full: html, text
    hack around some systems complaining about read result not being used even with cast
• src/makefile
  • lines changed 2, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/product/scripts/browserEnvironment.txt
  • lines changed 84, context: html, text, full: html, text
    rearrange the variables and clear up some definitions
  • lines changed 1, context: html, text, full: html, text
    test for LOGNAME not USER
• src/product/scripts/printEnv.pl
  • lines changed 19, context: html, text, full: html, text
    add information about how to use this as an hgTracks debug tool
• src/product/scripts/trashCleanMonitor.csh
  • lines changed 53, context: html, text, full: html, text
    this became .sh from this .csh
• src/product/scripts/trashCleanMonitor.sh
  • lines changed 53, context: html, text, full: html, text
    this should be .sh not .csh
  • lines changed 6, context: html, text, full: html, text
    need to create the logDir here too
• src/product/scripts/updateHtml.sh
  • lines changed 4, context: html, text, full: html, text
    DOCHOME should be DOCUMENTROOT
• src/utils/git-reports/git-reports.c
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    filter out release log commits
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    removed unneeded double-quote from commit message in doRLUpdate.csh script, so adjusted according here too
• src/utils/gtfToGenePred/gtfToGenePred.c
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    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/gtfToGenePred/makefile
  • lines changed 21, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/gtfToGenePred/tests/expected/basic.gp
  • lines changed 4, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/gtfToGenePred/tests/expected/basic.info
  • lines changed 5, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/gtfToGenePred/tests/expected/dups.gp
  • lines changed 2, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/gtfToGenePred/tests/expected/dups.out
  • lines changed 3, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/gtfToGenePred/tests/expected/ensembl.gp
  • lines changed 2, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/gtfToGenePred/tests/expected/ensembl.info
  • lines changed 3, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/gtfToGenePred/tests/expected/geneNameAsName2.gp
  • lines changed 2, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/gtfToGenePred/tests/expected/impliedStop.gp
  • lines changed 6, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/gtfToGenePred/tests/expected/impliedStop.info
  • lines changed 7, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/gtfToGenePred/tests/expected/splitStop.gp
  • lines changed 2, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/gtfToGenePred/tests/expected/srcPre.gp
  • lines changed 3, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/gtfToGenePred/tests/expected/srcPre.info
  • lines changed 4, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/gtfToGenePred/tests/input/basic.gtf
  • lines changed 14, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/gtfToGenePred/tests/input/dups.gtf
  • lines changed 19, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/gtfToGenePred/tests/input/ensembl.gtf
  • lines changed 12, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/gtfToGenePred/tests/input/flybase.gtf
  • lines changed 56, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/gtfToGenePred/tests/input/split.gtf
  • lines changed 5, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/gtfToGenePred/tests/input/splitStop.gtf
  • lines changed 34, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/gtfToGenePred/tests/makefile
  • lines changed 56, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
• src/utils/qa/getLastMonth.csh
  • lines changed 6, context: html, text, full: html, text
    fixed a small bug
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v240 final build
• src/utils/qa/weeklybld/updateCgiVersion.csh
  • lines changed 1, context: html, text, full: html, text
    removing unneeded quotes in commit message
• src/weblet/counter/makefile
  • lines changed 4, context: html, text, full: html, text
    fixup cygwin build

• lines changed: 5069
• files changed: 179