kent: changes by commit

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

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