kent: changes by file

branch to review (2009-12-14 to 2010-01-04) v222

• src/hg/encode/encodePatchTdb/encodePatchTdb.c
  • 1.2 lines changed: 803, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
  • 1.1 lines changed: 803, context: html, text, full: html, text
    file encodePatchTdb.c was initially added on branch viewInTheMiddle.
• src/hg/encode/encodePatchTdb/makefile
  • 1.2 lines changed: 18, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
  • 1.1 lines changed: 18, context: html, text, full: html, text
    file makefile was initially added on branch viewInTheMiddle.
• src/hg/hgChroms/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgTables/compositeTrack.c
  • 1.18 lines changed: 6, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgTables/hgTables.c
  • 1.188 lines changed: 6, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgTables/intersect.c
  • 1.52 lines changed: 10, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgTables/maf.c
  • 1.18 lines changed: 5, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgTables/mainPage.c
  • 1.145 lines changed: 5, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgTables/schema.c
  • 1.61 lines changed: 4, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgTables/wiggle.c
  • 1.76 lines changed: 11, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.511 lines changed: 13, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgTracks/hgTracks.c
  • 1.1617 lines changed: 37, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgTracks/hgTracks.h
  • 1.195 lines changed: 5, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgTracks/simpleTracks.c
  • 1.118 lines changed: 128, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgTracks/wigTrack.c
  • 1.101 lines changed: 4, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgc/hgc.c
  • 1.1584 lines changed: 36, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgc/wiggleClick.c
  • 1.33 lines changed: 2, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/inc/trackDb.h
  • 1.52 lines changed: 57, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/js/hui.js
  • 1.47 lines changed: 7, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/lib/cart.c
  • 1.115 lines changed: 40, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/lib/hVarSubst.c
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/lib/hdb.c
  • 1.417 lines changed: 208, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/lib/hui.c
  • 1.253 lines changed: 299, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/lib/trackDbCustom.c
  • 1.73 lines changed: 324, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/lib/wiggleCart.c
  • 1.37 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • 1.56 lines changed: 364, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/hgTrackDb/makefile
  • 1.32 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDb/tagTypes.tab
  • 1.5 lines changed: 13, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • 1.30 lines changed: 1105, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDb/drosophila/trackDb.ra
  • 1.84 lines changed: 911, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDb/human/encodeAffyChipSuper.html
  • 1.1 lines changed: 9, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/encodeEgaspSuper.html
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/encodeGencodeSuper.html
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/encodeStanfordChipSuper.html
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/encodeUvaDnaRepSuper.html
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/trackDb.encode.ra
  • 1.103 lines changed: 31, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
  • 1.102 lines changed: 7, context: html, text, full: html, text
    Moving encodeAffyChipSuper back down a level in directory to hg18 to serve as a test case that we can have supertracks in levels below their tracks. Have to keep the single child as well as the workaround for over-eager pruning in -strict mode in hgTrackDb.
  • 1.101 lines changed: 46, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.485 lines changed: 25, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDb/human/hg18/encodeAffyChipSuper.html
  • 1.9 lines changed: 56, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/hg18/encodeEgaspSuper.html
  • 1.11 lines changed: 257, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/hg18/encodeGencodeSuper.html
  • 1.9 lines changed: 160, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/hg18/encodeStanfordChipSuper.html
  • 1.9 lines changed: 33, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/hg18/encodeUvaDnaRepSuper.html
  • 1.10 lines changed: 43, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeChip.ra
  • 1.29 lines changed: 22, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
  • 1.28 lines changed: 2, context: html, text, full: html, text
    Adding comment as to nature of work-around.
  • 1.27 lines changed: 33, context: html, text, full: html, text
    Moving encodeAffyChipSuper back down a level in directory to hg18 to serve as a test case that we can have supertracks in levels below their tracks. Have to keep the single child as well as the workaround for over-eager pruning in -strict mode in hgTrackDb.
  • 1.26 lines changed: 18, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeChrom.ra
  • 1.10 lines changed: 9, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeCompAndVar.ra
  • 1.23 lines changed: 17, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeGenes.ra
  • 1.9 lines changed: 18, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeTxLevels.ra
  • 1.16 lines changed: 9, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.446 lines changed: 302, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.736 lines changed: 18312, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.79 lines changed: 956, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDb/mouse/mm8/trackDb.ra
  • 1.62 lines changed: 475, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.74 lines changed: 117, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDb/sacCer/trackDb.ra
  • 1.46 lines changed: 22, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDb/worm/trackDb.ra
  • 1.40 lines changed: 85, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDb/worm/ce6/trackDb.ra
  • 1.18 lines changed: 15, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDbPatch/trackDbPatch.c
  • 1.4 lines changed: 13, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/mouseStuff/axtToPsl/makefile
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/mouseStuff/mafFetch/makefile
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/mouseStuff/mafRanges/makefile
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/mouseStuff/mafToAxt/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/mouseStuff/mafToPsl/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/mouseStuff/subsetAxt/makefile
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/oneShot/freen/freen.c
  • 1.96 lines changed: 73, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/oneShot/makeTrackDbTagVals/makeTrackDbTagVals.c
  • 1.2 lines changed: 3, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/oneShot/tdbRewriteReduceReplaces/tdbRewriteReduceReplaces.c
  • 1.2 lines changed: 32, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/oneShot/tdbRewriteRemoveUnused/makefile
  • 1.2 lines changed: 18, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
  • 1.1 lines changed: 18, context: html, text, full: html, text
    file makefile was initially added on branch viewInTheMiddle.
• src/hg/oneShot/tdbRewriteRemoveUnused/tdbRewriteRemoveUnused.c
  • 1.2 lines changed: 571, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
  • 1.1 lines changed: 571, context: html, text, full: html, text
    file tdbRewriteRemoveUnused.c was initially added on branch viewInTheMiddle.
• src/hg/oneShot/tdbRewriteSortTags/tdbRewriteSortTags.c
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/oneShot/tdbRewriteViewsToSubtracks/tdbRewriteViewsToSubtracks.c
  • 1.5 lines changed: 31, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/pslCrudeCmp/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/ratStuff/mafFrags/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/ratStuff/mafOrtholog/makefile
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/spideyToPsl/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/utils/tdbQuery/tdbQuery.c
  • 1.26 lines changed: 51, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/zoo/pslToFa/makefile
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/inc/common.h
  • 1.166 lines changed: 3, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/lib/bigBed.c
  • 1.25 lines changed: 592, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/lib/cheapcgi.c
  • 1.128 lines changed: 0, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/lib/common.c
  • 1.143 lines changed: 13, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/utils/est2genomeToPsl/makefile
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/utils/faFlyBaseToUcsc/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/utils/faSimplify/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/utils/gffPeek/makefile
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/utils/spacedToTab/makefile
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/weblet/bottleneck/makefile
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.