CVS changes by file

branch to review (2010-05-04 to 2010-05-11) v231

• src/README
  • 1.23 lines changed: 2, context: html, text, full: html, text
    Getting explicit about not abbreviating 5 letter words.
• src/hg/archaeStuff/data/precomputed-tracks.tab
  • 1.8 lines changed: 3, context: html, text, full: html, text
    Added N.maritimus sRNA sequencing psl tracks
• src/hg/archaeStuff/tooltip/tooltip.c
  • 1.8 lines changed: 2, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/encode/DAFs/2.0/gisChiaPet.daf
  • 1.1 lines changed: 43, context: html, text, full: html, text
    Adding 2.0 versions of gisChaiPet data agreement.
• src/hg/encode/DAFs/2.0/gisChiaPetExample.ddf
  • 1.1 lines changed: 17, context: html, text, full: html, text
    Adding 2.0 versions of gisChaiPet data agreement.
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.238 lines changed: 3, context: html, text, full: html, text
    added missing organisms
  • 1.237 lines changed: 11, context: html, text, full: html, text
    Added 2 new protocols for HAIB TFBS
• src/hg/encode/encodeValidate/config/expVars.ra
  • 1.1 lines changed: 8, context: html, text, full: html, text
    added file for experimental variables
• src/hg/encode/utils/elandExtToSAM/elandExtToSAM.py
  • 1.4 lines changed: 20, context: html, text, full: html, text
    Now optional stdout output or save to gzip-ed file
  • 1.3 lines changed: 31, context: html, text, full: html, text
    Fixed bugs and added bzip2/gzip file input and gzip file output
• src/hg/encode/validateFiles/validateFiles.c
  • 1.41 lines changed: 135, context: html, text, full: html, text
    handle indels
• src/hg/hgCustom/hgCustom.c
  • 1.141 lines changed: 9, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgGenome/bedList.c
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgGenome/custom.c
  • 1.5 lines changed: 4, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgGenome/hgGenome.c
  • 1.67 lines changed: 2, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgGenome/import.c
  • 1.19 lines changed: 13, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgGenome/maf.c
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTables/bedList.c
  • 1.74 lines changed: 1, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTables/compositeTrack.c
  • 1.19 lines changed: 4, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTables/correlate.c
  • 1.79 lines changed: 7, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTables/custom.c
  • 1.47 lines changed: 7, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTables/hgTables.c
  • 1.194 lines changed: 24, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTables/identifiers.c
  • 1.30 lines changed: 1, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTables/intersect.c
  • 1.53 lines changed: 7, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTables/maf.c
  • 1.20 lines changed: 2, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTables/mainPage.c
  • 1.150 lines changed: 3, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTables/pal.c
  • 1.17 lines changed: 1, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTables/schema.c
  • 1.64 lines changed: 3, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTables/seqOut.c
  • 1.24 lines changed: 1, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTables/wiggle.c
  • 1.78 lines changed: 5, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTables/wikiTrack.c
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgText/hgText.c
  • 1.172 lines changed: 3, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTrackUi/encodePeakUi.c
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.524 lines changed: 98, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
  • 1.523 lines changed: 2, context: html, text, full: html, text
    Making container code use composite UI code for the moment.
  • 1.522 lines changed: 8, context: html, text, full: html, text
    Removing what looks to be an ancient Andy code-in-progress comment and a stray function prototype that went with it.
  • 1.521 lines changed: 11, context: html, text, full: html, text
    Simplifying/generalizing code that prints link to parent track's UI page.
  • 1.520 lines changed: 3, context: html, text, full: html, text
    Code to get container multiWig to go.
• src/hg/hgTracks/altGraphXTrack.c
  • 1.17 lines changed: 4, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/bamTrack.c
  • 1.31 lines changed: 2, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/bedGraph.c
  • 1.23 lines changed: 3, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/bedTrack.c
  • 1.25 lines changed: 14, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/bigBedTrack.c
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/bigWigTrack.c
  • 1.11 lines changed: 2, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/cds.c
  • 1.106 lines changed: 6, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/cgapSageTrack.c
  • 1.15 lines changed: 2, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/chainTrack.c
  • 1.39 lines changed: 6, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/chromGraphTrack.c
  • 1.21 lines changed: 5, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/config.c
  • 1.92 lines changed: 5, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/container.c
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
  • 1.2 lines changed: 44, context: html, text, full: html, text
    Separating out multiWigs into a separate module from container.
  • 1.1 lines changed: 97, context: html, text, full: html, text
    Code to get container multiWig to go.
• src/hg/hgTracks/container.h
  • 1.1 lines changed: 13, context: html, text, full: html, text
    Separating out multiWigs into a separate module from container.
• src/hg/hgTracks/contigTrack.c
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/cutterTrack.c
  • 1.15 lines changed: 5, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/cytoBandTrack.c
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/encode.c
  • 1.24 lines changed: 2, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/expRatioTracks.c
  • 1.49 lines changed: 21, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/factorSource.c
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
  • 1.6 lines changed: 14, context: html, text, full: html, text
    Code to get container multiWig to go.
• src/hg/hgTracks/goldTrack.c
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/hapmapTrack.c
  • 1.48 lines changed: 16, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/hgTracks.c
  • 1.1647 lines changed: 86, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
  • 1.1646 lines changed: 3, context: html, text, full: html, text
    Code to get container multiWig to go.
• src/hg/hgTracks/hgTracks.h
  • 1.210 lines changed: 2, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
  • 1.209 lines changed: 3, context: html, text, full: html, text
    Improving some comments
  • 1.208 lines changed: 7, context: html, text, full: html, text
    Code to get container multiWig to go.
• src/hg/hgTracks/imageV2.c
  • 1.27 lines changed: 8, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/loweLabTracks.c
  • 1.32 lines changed: 5, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/mafTrack.c
  • 1.65 lines changed: 6, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/makeItemsTrack.c
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/makefile
  • 1.93 lines changed: 1, context: html, text, full: html, text
    Separating out multiWigs into a separate module from container.
  • 1.92 lines changed: 1, context: html, text, full: html, text
    Code to get container multiWig to go.
• src/hg/hgTracks/multiWig.c
  • 1.2 lines changed: 14, context: html, text, full: html, text
    Making calculations that all wigs below share same limits work better.
  • 1.1 lines changed: 67, context: html, text, full: html, text
    Separating out multiWigs into a separate module from container.
• src/hg/hgTracks/netTrack.c
  • 1.27 lines changed: 3, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/pslTrack.c
  • 1.34 lines changed: 7, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/retroGene.c
  • 1.19 lines changed: 7, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/rmskTrack.c
  • 1.14 lines changed: 3, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/rnaFoldTrack.c
  • 1.9 lines changed: 4, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/rnaPLFoldTrack.c
  • 1.9 lines changed: 5, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/sampleTracks.c
  • 1.10 lines changed: 26, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/searchTracks.c
  • 1.2 lines changed: 5, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/simpleTracks.c
  • 1.139 lines changed: 104, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
  • 1.138 lines changed: 27, context: html, text, full: html, text
    Code to get container multiWig to go.
• src/hg/hgTracks/switchGear.c
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/transMapTracks.c
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/transcriptome.c
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/variation.c
  • 1.147 lines changed: 27, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/wigCommon.h
  • 1.11 lines changed: 7, context: html, text, full: html, text
    Separating out multiWigs into a separate module from container.
• src/hg/hgTracks/wigMafTrack.c
  • 1.146 lines changed: 20, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
  • 1.145 lines changed: 22, context: html, text, full: html, text
    Fixing wigMaf tracks by being a little more careful about how the wiggle subtracks are manufactured.
• src/hg/hgTracks/wigTrack.c
  • 1.108 lines changed: 20, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
  • 1.107 lines changed: 22, context: html, text, full: html, text
    Separating out multiWigs into a separate module from container.
• src/hg/hgTracks/wiki.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgTracks/wikiTrack.c
  • 1.21 lines changed: 9, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgc/bamClick.c
  • 1.21 lines changed: 4, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgc/bigBedClick.c
  • 1.11 lines changed: 2, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgc/cgapSageClick.c
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgc/dbRIP.c
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgc/encodeClick.c
  • 1.15 lines changed: 2, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgc/expClick.c
  • 1.25 lines changed: 3, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgc/hgc.c
  • 1.1620 lines changed: 348, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgc/hgdpClick.c
  • 1.9 lines changed: 2, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgc/lowelab.c
  • 1.50 lines changed: 70, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgc/mafClick.c
  • 1.61 lines changed: 15, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgc/makeItemsClick.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgc/mgcClick.c
  • 1.33 lines changed: 2, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgc/parClick.c
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgc/regMotif.c
  • 1.22 lines changed: 6, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgc/retroClick.c
  • 1.15 lines changed: 1, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgc/rnaFoldClick.c
  • 1.9 lines changed: 2, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgc/transMapClick.c
  • 1.13 lines changed: 2, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/hgc/wiggleClick.c
  • 1.34 lines changed: 7, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/inc/hPrint.h
  • 1.11 lines changed: 3, context: html, text, full: html, text
    new function hPrintEncodeNonBreak to protect against problems with <>;" in output, problem was recently uncovered by hgNearTest
• src/hg/inc/trackDb.h
  • 1.59 lines changed: 5, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
  • 1.58 lines changed: 5, context: html, text, full: html, text
    Adding trackDbFieldsFromSettings
• src/hg/inc/wiggle.h
  • 1.90 lines changed: 12, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/instinct/bioInt2/grabData.c
  • 1.8 lines changed: 9, context: html, text, full: html, text
    
• src/hg/instinct/extractData/extractData.c
  • 1.9 lines changed: 50, context: html, text, full: html, text
    
  • 1.8 lines changed: 2, context: html, text, full: html, text
    
• src/hg/instinct/extractData/transpose.py
  • 1.2 lines changed: 1, context: html, text, full: html, text
    
  • 1.1 lines changed: 32, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/drawingCode.c
  • 1.83 lines changed: 1, context: html, text, full: html, text
    fixed missing data drawing bug
  • 1.82 lines changed: 9, context: html, text, full: html, text
    fixed bugs
  • 1.81 lines changed: 82, context: html, text, full: html, text
    added new way of accessing clinical features
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.su2c_processed.ra
  • 1.2 lines changed: 56, context: html, text, full: html, text
    Adding downsample tables and fixing CNV datasets
• src/hg/instinct/inc/featuresLib.h
  • 1.16 lines changed: 3, context: html, text, full: html, text
    added new way of accessing clinical features
• src/hg/instinct/lib/featuresLib.c
  • 1.34 lines changed: 5, context: html, text, full: html, text
    fixed missing data drawing bug
  • 1.33 lines changed: 3, context: html, text, full: html, text
    fixed bugs
  • 1.32 lines changed: 40, context: html, text, full: html, text
    added new way of accessing clinical features
• src/hg/instinct/lib/hgHeatmapLib.c
  • 1.70 lines changed: 8, context: html, text, full: html, text
    fixed bugs
• src/hg/instinct/lib/sortFeatures.c
  • 1.7 lines changed: 4, context: html, text, full: html, text
    fixed sorting bug
  • 1.6 lines changed: 59, context: html, text, full: html, text
    fixed bugs
  • 1.5 lines changed: 12, context: html, text, full: html, text
    added new way of accessing clinical features
• src/hg/js/hgTracks.js
  • 1.67 lines changed: 1, context: html, text, full: html, text
    Got tired of seeing the error of 'hgTracksInitTracks not defined'.
• src/hg/lib/cart.c
  • 1.119 lines changed: 7, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/lib/chromGraphFactory.c
  • 1.18 lines changed: 2, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/lib/customFactory.c
  • 1.124 lines changed: 20, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/lib/customTrack.c
  • 1.181 lines changed: 13, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/lib/gbStatus.as
  • 1.2 lines changed: 19, context: html, text, full: html, text
    Obsoleted by Mark's improvements in genbankTables.as.
• src/hg/lib/genePred.c
  • 1.103 lines changed: 2, context: html, text, full: html, text
    Fixing indentation.
• src/hg/lib/hPrint.c
  • 1.11 lines changed: 9, context: html, text, full: html, text
    new function hPrintEncodeNonBreak to protect against problems with <>;" in output, problem was recently uncovered by hgNearTest
• src/hg/lib/hVarSubst.c
  • 1.8 lines changed: 5, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/lib/hdb.c
  • 1.426 lines changed: 8, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
  • 1.425 lines changed: 3, context: html, text, full: html, text
    Code to get container multiWig to go.
• src/hg/lib/hgMaf.c
  • 1.15 lines changed: 1, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/lib/hui.c
  • 1.284 lines changed: 81, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
  • 1.283 lines changed: 2, context: html, text, full: html, text
    removing commented out testing code.
• src/hg/lib/mdb.c
  • 1.7 lines changed: 8, context: html, text, full: html, text
    Improve multi-var query
  • 1.6 lines changed: 3, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/lib/metaTbl.c
  • 1.13 lines changed: 3, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/lib/netCart.c
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/lib/pcrResult.c
  • 1.12 lines changed: 2, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/lib/tests/customTrackTester.c
  • 1.5 lines changed: 7, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/lib/trackDb.as
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/lib/trackDb.c
  • 1.11 lines changed: 4, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/lib/trackDbCustom.c
  • 1.87 lines changed: 102, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
  • 1.86 lines changed: 96, context: html, text, full: html, text
    Code to get container multiWig to go.
• src/hg/lib/web.c
  • 1.172 lines changed: 2, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/lib/wiggleCart.c
  • 1.39 lines changed: 3, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/lib/wiggleUtils.c
  • 1.56 lines changed: 1, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/makeDb/doc/calJac3.txt
  • 1.9 lines changed: 3, context: html, text, full: html, text
    correct FTP NCBI address
• src/hg/makeDb/doc/encodeDccHg18/mapability.txt
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Updated release notes for CRG subtracks of Mapability track.
• src/hg/makeDb/doc/encodeDccHg18/yaleChIPseq.release3.notes.txt
  • 1.2 lines changed: 6, context: html, text, full: html, text
    Two files were accidentally listed as deprecated but are actually untouched
• src/hg/makeDb/doc/encodeDccHg19/mapability.txt
  • 1.1 lines changed: 8, context: html, text, full: html, text
    Mapabilty track release notes for first release.
• src/hg/makeDb/doc/encodeHg18.txt
  • 1.34 lines changed: 10, context: html, text, full: html, text
    Removed documentation about CRG Mapability track as this is from the whole genome ENCODE and this document is for the pilot project.
• src/hg/makeDb/doc/encodeHg19.txt
  • 1.3 lines changed: 14, context: html, text, full: html, text
    Removed file as notes for the whole genome ENCODE are in another directory.
• src/hg/makeDb/doc/felCatV17e.txt
  • 1.13 lines changed: 130, context: html, text, full: html, text
    Complete multiz6way
  • 1.12 lines changed: 26, context: html, text, full: html, text
    human proteins
  • 1.11 lines changed: 160, context: html, text, full: html, text
    starting human proteins
• src/hg/makeDb/doc/hg18.txt
  • 1.415 lines changed: 4, context: html, text, full: html, text
    Adding a few more steps to regulation track.
  • 1.414 lines changed: 30, context: html, text, full: html, text
    Starting to put in instructions for the encode regulatory track. Will need polishing, but at least this will help me remember what I did.....
• src/hg/makeDb/doc/oviAri1.txt
  • 1.6 lines changed: 45, context: html, text, full: html, text
    Lastz finished
• src/hg/makeDb/genbank/etc/rr.dbs
  • 1.92 lines changed: 1, context: html, text, full: html, text
    turning on genbank updates for susScr2
• src/hg/makeDb/hgBedsToBedExps/hgBedsToBedExps.c
  • 1.6 lines changed: 8, context: html, text, full: html, text
    Making it so scores go from 0-1000
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Making it so that output scores are integer rather than floating point since they are in 0-1000 range.
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Removing unused variable.
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.105 lines changed: 53, context: html, text, full: html, text
    Fixing incorrect sample ordering, and added new gray cell lines names
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • 1.67 lines changed: 37, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
  • 1.66 lines changed: 4, context: html, text, full: html, text
    Removed some debugging statements.
  • 1.65 lines changed: 47, context: html, text, full: html, text
    Code to get container multiWig to go.
• src/hg/makeDb/schema/all.joiner
  • 1.799 lines changed: 15, context: html, text, full: html, text
    Fixed probelems with consIndels and danRerBacSangerName rules. For ecores and danRer3 phastConsElements, moved these into the highest level of the hierarchy for the genome in tbalesIgored.
  • 1.798 lines changed: 1, context: html, text, full: html, text
    added broadStemChip to mouse ignore list
  • 1.797 lines changed: 2, context: html, text, full: html, text
    Changed danRerBacSangerName rule to be specific for danRer3 and danRer4.
  • 1.796 lines changed: 20, context: html, text, full: html, text
    Added ecores and phastCons tables to list of tables to be ignored. Added new rules for the consIndels track and the bacCloneAlias tables from danRer.
  • 1.795 lines changed: 2, context: html, text, full: html, text
    adding ctgPos2 to tables ignored
  • 1.794 lines changed: 2, context: html, text, full: html, text
    add new cat to human proteins
• src/hg/makeDb/trackDb/alpaca/vicPac1/trackDb.ra
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/ancestor/borEut13/trackDb.ra
  • 1.11 lines changed: 2, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/ancestor/canHg10/trackDb.ra
  • 1.12 lines changed: 1, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/ancestor/canHg11/trackDb.ra
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/ancestor/canHg12/trackDb.ra
  • 1.9 lines changed: 2, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/ancestor/canHg4/trackDb.ra
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/ancestor/canHg9/trackDb.ra
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/ancestor/car46/trackDb.ra
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/ancestor/catArr1/trackDb.ra
  • 1.8 lines changed: 2, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/ancestor/euaGli13/trackDb.ra
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/ancestor/gliRes13/trackDb.ra
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/ancestor/homIni13/trackDb.ra
  • 1.10 lines changed: 3, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/ancestor/homIni14/trackDb.ra
  • 1.9 lines changed: 2, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/ancestor/homIni20/trackDb.ra
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/ancestor/homPan20/trackDb.ra
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/ancestor/priMat13/trackDb.ra
  • 1.9 lines changed: 2, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/ancestor/rodEnt13/trackDb.ra
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/ancestor/trackDb.ra
  • 1.13 lines changed: 4, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/apis/trackDb.ra
  • 1.17 lines changed: 29, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/armadillo/dasNov1/trackDb.ra
  • 1.5 lines changed: 11, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/armadillo/dasNov2/trackDb.ra
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/baboon/papHam1/trackDb.ra
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/cat/felCat3/trackDb.ra
  • 1.28 lines changed: 30, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/cat/felCatV17e/ctgPos2.html
  • 1.1 lines changed: 9, context: html, text, full: html, text
    adding scaffold track html
• src/hg/makeDb/trackDb/cat/felCatV17e/trackDb.ra
  • 1.4 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
  • 1.3 lines changed: 25, context: html, text, full: html, text
    Add multiz6way
• src/hg/makeDb/trackDb/cat/trackDb.ra
  • 1.16 lines changed: 3, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/cow/bosTau1/trackDb.ra
  • 1.21 lines changed: 28, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/cow/bosTau2/trackDb.ra
  • 1.12 lines changed: 30, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/cow/bosTau3/trackDb.ra
  • 1.10 lines changed: 30, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/cow/bosTau4/trackDb.ra
  • 1.23 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/dog/canFamPoodle1/trackDb.ra
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra
  • 1.25 lines changed: 5, context: html, text, full: html, text
    remove oviAri1
  • 1.24 lines changed: 5, context: html, text, full: html, text
    Add Sheep oviAri1
  • 1.23 lines changed: 1, context: html, text, full: html, text
    changing chainMinScore gap to 3000 for calJac3 as I was told to do by the script
• src/hg/makeDb/trackDb/dolphin/turTru1/trackDb.ra
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/drosophila/dm1/trackDb.ra
  • 1.65 lines changed: 14, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
  • 1.64 lines changed: 3, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/drosophila/dm2/trackDb.ra
  • 1.65 lines changed: 14, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
  • 1.64 lines changed: 29, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/drosophila/dp2/trackDb.ra
  • 1.14 lines changed: 28, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/drosophila/dp3/trackDb.ra
  • 1.18 lines changed: 14, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/drosophila/droAna1/trackDb.ra
  • 1.17 lines changed: 28, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/drosophila/droAna2/trackDb.ra
  • 1.13 lines changed: 16, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/drosophila/droEre1/trackDb.ra
  • 1.15 lines changed: 28, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/drosophila/droGri1/trackDb.ra
  • 1.10 lines changed: 28, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/drosophila/droMoj1/trackDb.ra
  • 1.16 lines changed: 28, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/drosophila/droMoj2/trackDb.ra
  • 1.8 lines changed: 28, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/drosophila/droSim1/trackDb.ra
  • 1.21 lines changed: 14, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/drosophila/droVir1/trackDb.ra
  • 1.16 lines changed: 28, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/drosophila/droVir2/trackDb.ra
  • 1.8 lines changed: 28, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/drosophila/droYak1/trackDb.ra
  • 1.19 lines changed: 14, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/drosophila/trackDb.ra
  • 1.89 lines changed: 76, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/elephant/loxAfr1/trackDb.ra
  • 1.5 lines changed: 15, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/elephant/loxAfr2/trackDb.ra
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/elephant/loxAfr3/trackDb.ra
  • 1.5 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/fugu/trackDb.ra
  • 1.82 lines changed: 14, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/gorilla/gorGor1/trackDb.ra
  • 1.4 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/gorilla/gorGor2/trackDb.ra
  • 1.2 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.ra
  • 1.12 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/hedgehog/eriEur1/trackDb.ra
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/hiv/trackDb.ra
  • 1.8 lines changed: 28, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/human/hg16/trackDb.encode.ra
  • 1.16 lines changed: 120, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/human/hg16/trackDb.ra
  • 1.591 lines changed: 11, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/human/hg17/trackDb.encode.ra
  • 1.182 lines changed: 360, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • 1.458 lines changed: 71, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/human/hg18/mdbBroad.ra
  • 1.4 lines changed: 11164, context: html, text, full: html, text
    Moved all of this meadata to metaDb subdir and named by composite
• src/hg/makeDb/trackDb/human/hg18/mdbHaibTfbs.ra
  • 1.9 lines changed: 16385, context: html, text, full: html, text
    Moved all of this meadata to metaDb subdir and named by composite
• src/hg/makeDb/trackDb/human/hg18/mdbOpenChrom.ra
  • 1.5 lines changed: 12139, context: html, text, full: html, text
    Moved all of this meadata to metaDb subdir and named by composite
• src/hg/makeDb/trackDb/human/hg18/mdbUwDgf.ra
  • 1.2 lines changed: 469, context: html, text, full: html, text
    Moved all of this meadata to metaDb subdir and named by composite
• src/hg/makeDb/trackDb/human/hg18/mdbUwDnase.ra
  • 1.2 lines changed: 7608, context: html, text, full: html, text
    Moved all of this meadata to metaDb subdir and named by composite
• src/hg/makeDb/trackDb/human/hg18/mdbUwHist.ra
  • 1.3 lines changed: 12796, context: html, text, full: html, text
    Moved all of this meadata to metaDb subdir and named by composite
• src/hg/makeDb/trackDb/human/hg18/mdbYaleTfbs.ra
  • 1.9 lines changed: 24601, context: html, text, full: html, text
    Moved all of this meadata to metaDb subdir and named by composite
  • 1.8 lines changed: 45, context: html, text, full: html, text
    Added 2 missing fastqs
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeBroadChipSeq.ra
  • 1.1 lines changed: 11164, context: html, text, full: html, text
    Moved all of this meadata to metaDb subdir and named by composite
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeChromatinMap.ra
  • 1.1 lines changed: 12139, context: html, text, full: html, text
    Moved all of this meadata to metaDb subdir and named by composite
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeHudsonalphaChipSeq.ra
  • 1.1 lines changed: 16385, context: html, text, full: html, text
    Moved all of this meadata to metaDb subdir and named by composite
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeHudsonalphaRnaSeq.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Magic needed fixing
  • 1.1 lines changed: 279, context: html, text, full: html, text
    Moved all of this meadata to metaDb subdir and named by composite
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeUwChIPSeq.ra
  • 1.1 lines changed: 12796, context: html, text, full: html, text
    Moved all of this meadata to metaDb subdir and named by composite
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeUwDGF.ra
  • 1.1 lines changed: 469, context: html, text, full: html, text
    Moved all of this meadata to metaDb subdir and named by composite
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeUwDnaseSeq.ra
  • 1.1 lines changed: 7608, context: html, text, full: html, text
    Moved all of this meadata to metaDb subdir and named by composite
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeYaleChIPseq.ra
  • 1.1 lines changed: 24601, context: html, text, full: html, text
    Moved all of this meadata to metaDb subdir and named by composite
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeChip.ra
  • 1.30 lines changed: 182, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeChrom.ra
  • 1.11 lines changed: 34, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeCompAndVar.ra
  • 1.24 lines changed: 5, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeTxLevels.ra
  • 1.17 lines changed: 32, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.484 lines changed: 25, context: html, text, full: html, text
    More work on encode regulatory track.
  • 1.483 lines changed: 1, context: html, text, full: html, text
    Making subtracks of the regulatory wiggle configurable.
  • 1.482 lines changed: 340, context: html, text, full: html, text
    Adding regulatory track components. Changing subTrack to parent.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.964 lines changed: 1, context: html, text, full: html, text
    set maxItems to 20. This resolves the 32,000 bit image problem
  • 1.963 lines changed: 6, context: html, text, full: html, text
    Corrections, clarifications; this track doesnt yet actually contain footprints
  • 1.962 lines changed: 9, context: html, text, full: html, text
    some Orchid track changes
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncodeRikenRawSignal.ra
  • 1.2 lines changed: 22, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBuOrchid.html
  • 1.1 lines changed: 138, context: html, text, full: html, text
    track description
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.beta.ra
  • 1.4 lines changed: 143, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.alpha.ra
  • 1.14 lines changed: 80, context: html, text, full: html, text
    releasing beta
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.alpha.ra
  • 1.7 lines changed: 60, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.beta.ra
  • 1.3 lines changed: 60, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDGF.html
  • 1.8 lines changed: 7, context: html, text, full: html, text
    Corrections, clarifications; this track doesnt yet actually contain footprints
• src/hg/makeDb/trackDb/human/hg19/mdbHaibTfbs.ra
  • 1.3 lines changed: 1169, context: html, text, full: html, text
    Move 3 mdb RA files to metaDb subdir
  • 1.2 lines changed: 281, context: html, text, full: html, text
    Updated metadata file for HAIB TFBS track to include two new submissions from pipeline (1180,1188)
• src/hg/makeDb/trackDb/human/hg19/metaDb/wgEncodeHaibTfbs.ra
  • 1.1 lines changed: 1169, context: html, text, full: html, text
    Move 3 mdb RA files to metaDb subdir
• src/hg/makeDb/trackDb/human/hg19/metaDb/wgEncodeSydhHistone.ra
  • 1.1 lines changed: 467, context: html, text, full: html, text
    Move 3 mdb RA files to metaDb subdir
• src/hg/makeDb/trackDb/human/hg19/metaDb/wgEncodeSydhTfbs.ra
  • 1.1 lines changed: 2505, context: html, text, full: html, text
    Move 3 mdb RA files to metaDb subdir
• src/hg/makeDb/trackDb/human/hg19/trackDb.enc.ra
  • 1.20 lines changed: 1, context: html, text, full: html, text
    SYDH Histone: Updated Long label of composite track to be consistent with long lable from SYDH TFBS
  • 1.19 lines changed: 7, context: html, text, full: html, text
    SYDH TFBS: Added prelimary default view limits for Signal track.
  • 1.18 lines changed: 3, context: html, text, full: html, text
    SYDH Histone: Changed view limits of signals from devault. Turned Control subtrack off on defult.
  • 1.17 lines changed: 128, context: html, text, full: html, text
    Track SYDH TFBS, removed signal filter tags for Signal bigwig files. Track SYDH Histone: Initial checkin of Composite and subtrack.
  • 1.16 lines changed: 1, context: html, text, full: html, text
    take out misspelling
  • 1.15 lines changed: 31, context: html, text, full: html, text
    Track SYDH TFBS: Updated shortlabels to be 16 characters long and aligned.
  • 1.14 lines changed: 120, context: html, text, full: html, text
    Updated HAIB TFBS track to include two new submission (1180,1188). Modified Short Labels to 16 chracters.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.117 lines changed: 31, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.html
  • 1.1 lines changed: 49, context: html, text, full: html, text
    SYDH Histone: Initial Description page, with place holding values to be filled in once provided.
• src/hg/makeDb/trackDb/human/ntHumChimpCodingDiff.html
  • 1.3 lines changed: 2, context: html, text, full: html, text
    A few more tweaks to refs.
  • 1.2 lines changed: 6, context: html, text, full: html, text
    Updated refs.
  • 1.1 lines changed: 47, context: html, text, full: html, text
    Migrated Neandertal track descriptions from genome-nt.
• src/hg/makeDb/trackDb/human/ntMito.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    A few more tweaks to refs.
  • 1.2 lines changed: 3, context: html, text, full: html, text
    Updated refs.
  • 1.1 lines changed: 48, context: html, text, full: html, text
    Migrated Neandertal track descriptions from genome-nt.
• src/hg/makeDb/trackDb/human/ntModernHumans.html
  • 1.3 lines changed: 2, context: html, text, full: html, text
    A few more tweaks to refs.
  • 1.2 lines changed: 6, context: html, text, full: html, text
    Updated refs.
  • 1.1 lines changed: 137, context: html, text, full: html, text
    Migrated Neandertal track descriptions from genome-nt.
• src/hg/makeDb/trackDb/human/ntOoaHaplo.html
  • 1.3 lines changed: 2, context: html, text, full: html, text
    A few more tweaks to refs.
  • 1.2 lines changed: 11, context: html, text, full: html, text
    Updated refs.
  • 1.1 lines changed: 101, context: html, text, full: html, text
    Migrated Neandertal track descriptions from genome-nt.
• src/hg/makeDb/trackDb/human/ntSssSnps.html
  • 1.3 lines changed: 3, context: html, text, full: html, text
    A few more tweaks to refs.
  • 1.2 lines changed: 9, context: html, text, full: html, text
    Updated refs.
  • 1.1 lines changed: 72, context: html, text, full: html, text
    Migrated Neandertal track descriptions from genome-nt.
• src/hg/makeDb/trackDb/human/ntSssTop5p.html
  • 1.4 lines changed: 3, context: html, text, full: html, text
    A few more tweaks to refs.
  • 1.3 lines changed: 8, context: html, text, full: html, text
    Updated refs.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Tweak requested by Ed/b0b: drop 'previous'.
  • 1.1 lines changed: 62, context: html, text, full: html, text
    Migrated Neandertal track descriptions from genome-nt.
• src/hg/makeDb/trackDb/human/ntSssZScorePMVar.html
  • 1.4 lines changed: 3, context: html, text, full: html, text
    A few more tweaks to refs.
  • 1.3 lines changed: 5, context: html, text, full: html, text
    Updated refs.
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Tweak requested by Ed/b0b: drop 'previous'.
  • 1.1 lines changed: 58, context: html, text, full: html, text
    Migrated Neandertal track descriptions from genome-nt.
• src/hg/makeDb/trackDb/human/trackDb.encode.ra
  • 1.104 lines changed: 475, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/human/trackDb.nt.ra
  • 1.1 lines changed: 137, context: html, text, full: html, text
    Migrated Neandertal track descriptions from genome-nt.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.533 lines changed: 1, context: html, text, full: html, text
    and make that beta,public.
  • 1.532 lines changed: 1, context: html, text, full: html, text
    Oops, needed to use release public instead of release beta for DGV old label.
  • 1.531 lines changed: 207, context: html, text, full: html, text
    Changing subTrack to parent.
  • 1.530 lines changed: 20, context: html, text, full: html, text
    Migrated Neandertal track descriptions from genome-nt.
• src/hg/makeDb/trackDb/kangarooRat/dipOrd1/trackDb.ra
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/lamprey/trackDb.ra
  • 1.9 lines changed: 16, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/lancelet/trackDb.ra
  • 1.3 lines changed: 16, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/lizard/anoCar1/trackDb.ra
  • 1.4 lines changed: 17, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/loadTracks
  • 1.21 lines changed: 1, context: html, text, full: html, text
    Uncommenting tdbQuery -check execution
• src/hg/makeDb/trackDb/marmoset/calJac1/trackDb.ra
  • 1.15 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.chainNet.ra
  • 1.4 lines changed: 4, context: html, text, full: html, text
    moving chain/Net overrides for rheMac2 down one level for calJac3. interferring with calJac1 when on marmoset level
  • 1.3 lines changed: 4, context: html, text, full: html, text
    adding matrix and chainMinScore overrides for ponAbe2 in calJac3
  • 1.2 lines changed: 2, context: html, text, full: html, text
    removing unecessary lines from chainNetPanTro2 override
  • 1.1 lines changed: 5, context: html, text, full: html, text
    adding a .chainNet.ra file to override chainNets for panTro2
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
  • 1.7 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
  • 1.6 lines changed: 1, context: html, text, full: html, text
    correct wrong longLableName
  • 1.5 lines changed: 2, context: html, text, full: html, text
    adding include line to include new trackDb.chainNet.ra file
• src/hg/makeDb/trackDb/marmoset/trackDb.chainNet.ra
  • 1.11 lines changed: 2, context: html, text, full: html, text
    moving chain/Net overrides for rheMac2 down one level for calJac3. interferring with calJac1 when on marmoset level
• src/hg/makeDb/trackDb/medaka/oryLat2/trackDb.ra
  • 1.9 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/megabat/pteVam1/trackDb.ra
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/microbat/myoLuc1/trackDb.ra
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/mouse/mm7/trackDb.ra
  • 1.69 lines changed: 2, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/mouse/mm8/trackDb.broadStem.ra
  • 1.15 lines changed: 28, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/mouse/mm8/trackDb.ra
  • 1.70 lines changed: 49, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/mouse/mm9/mdbSydhTfbs.txt
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Moved to metaDb subdir
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/wgEncodeSydhTfbs.ra
  • 1.1 lines changed: 572, context: html, text, full: html, text
    Initial check in of Cricket's SYDH TFBS on mm9
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.enc.ra
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Change short labels to match human
  • 1.8 lines changed: 4, context: html, text, full: html, text
    Minor changes in long labels to be consistenet with vsmalladi
  • 1.7 lines changed: 20, context: html, text, full: html, text
    Mostly modifying spelling errors and label changes. The Signal view defaults have been changed.
  • 1.6 lines changed: 54, context: html, text, full: html, text
    Now there is a an improved checker for cruff in the Signal Tracks. I have removed the signalFilter line from the Signal tracks and now it should make properly.
  • 1.5 lines changed: 17, context: html, text, full: html, text
    Changing short labels to be more readable
  • 1.4 lines changed: 10, context: html, text, full: html, text
    Added the inputs with different controls as different factors in the matrix.
  • 1.3 lines changed: 43, context: html, text, full: html, text
    Fix the mm9 SYDH encode tracks to show the drop down menus for Peaks and Signal and to hide the UI for Signal and to display all of the signal tracks.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.91 lines changed: 24, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • 1.214 lines changed: 5, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/mouseLemur/micMur1/trackDb.ra
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/ntSeqContigs.html
  • 1.3 lines changed: 5, context: html, text, full: html, text
    A few more tweaks to refs.
  • 1.2 lines changed: 5, context: html, text, full: html, text
    Updated Green et al. ref.
  • 1.1 lines changed: 126, context: html, text, full: html, text
    Migrated Neandertal track descriptions from genome-nt.
• src/hg/makeDb/trackDb/ntSeqReads.html
  • 1.3 lines changed: 4, context: html, text, full: html, text
    A few more tweaks to refs.
  • 1.2 lines changed: 7, context: html, text, full: html, text
    Updated Green et al. ref.
  • 1.1 lines changed: 122, context: html, text, full: html, text
    Migrated Neandertal track descriptions from genome-nt.
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra
  • 1.35 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/opossum/trackDb.ra
  • 1.56 lines changed: 6, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/orangutan/ponAbe1/trackDb.ra
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/other/nemVec1/trackDb.ra
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/panda/ailMel1/trackDb.ra
  • 1.2 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/pig/trackDb.chainNet.ra
  • 1.3 lines changed: 8, context: html, text, full: html, text
    adding visibility overrides to make the default position for susScr2. Did affect susSCr1, but figured since it was only on dev this was ok
• src/hg/makeDb/trackDb/pig/trackDb.ra
  • 1.3 lines changed: 6, context: html, text, full: html, text
    adding visibility overrides to make the default position for susScr2. Did affect susSCr1, but figured since it was only on dev this was ok
• src/hg/makeDb/trackDb/pika/ochPri2/trackDb.ra
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/platypus/ornAna1/trackDb.ra
  • 1.21 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/rabbit/oryCun1/trackDb.ra
  • 1.7 lines changed: 16, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/rabbit/oryCun2/ctgPos2.html
  • 1.1 lines changed: 8, context: html, text, full: html, text
    adding override of scaffold html with correct info
• src/hg/makeDb/trackDb/rabbit/oryCun2/trackDb.ra
  • 1.4 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/rat/trackDb.ra
  • 1.82 lines changed: 2, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/rhesus/trackDb.ra
  • 1.25 lines changed: 29, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/rockHyrax/proCap1/trackDb.ra
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/rockHyrax/proCav1/trackDb.ra
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/sacCer/trackDb.ra
  • 1.49 lines changed: 6, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/sars/sc1/trackDb.ra
  • 1.17 lines changed: 16, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/seaHare/aplCal1/trackDb.ra
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/sheep/oviAri1/description.html
  • 1.6 lines changed: 4, context: html, text, full: html, text
    Photo credit
• src/hg/makeDb/trackDb/sheep/oviAri1/trackDb.ra
  • 1.2 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/shrew/sorAra1/trackDb.ra
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/sloth/choHof1/trackDb.ra
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/squirrel/speTri1/trackDb.ra
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/squirt/ci1/trackDb.ra
  • 1.54 lines changed: 29, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/squirt/ci2/trackDb.ra
  • 1.11 lines changed: 29, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/squirt/cioSav1/trackDb.ra
  • 1.7 lines changed: 26, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/squirt/cioSav2/trackDb.ra
  • 1.10 lines changed: 29, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/squirt/trackDb.ra
  • 1.15 lines changed: 14, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/tagTypes.tab
  • 1.19 lines changed: 1, context: html, text, full: html, text
    Making any type take maxItems.
  • 1.18 lines changed: 1, context: html, text, full: html, text
    add broadPeak to types acceptable to maxItems
  • 1.17 lines changed: 1, context: html, text, full: html, text
    Adding table tag
  • 1.16 lines changed: 2, context: html, text, full: html, text
    Adding a few new tags.
  • 1.15 lines changed: 8, context: html, text, full: html, text
    Added various tag types for Neandertal tracks.
  • 1.14 lines changed: 2, context: html, text, full: html, text
    add a couple of variables used in the Gencode track
• src/hg/makeDb/trackDb/tarsier/tarSyr1/trackDb.ra
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/tenrec/echTel1/trackDb.ra
  • 1.7 lines changed: 16, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/tetraodon/trackDb.ra
  • 1.62 lines changed: 14, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • 1.93 lines changed: 312, context: html, text, full: html, text
    Changing subTrack to parent.
  • 1.92 lines changed: 3, context: html, text, full: html, text
    Correct cases for oviAri1
  • 1.91 lines changed: 53, context: html, text, full: html, text
    Add oviAri1 Sheep
• src/hg/makeDb/trackDb/trackDb.nt.ra
  • 1.1 lines changed: 126, context: html, text, full: html, text
    Migrated Neandertal track descriptions from genome-nt.
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.630 lines changed: 2, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
  • 1.629 lines changed: 0, context: html, text, full: html, text
    Changing subTrack to parent.
  • 1.628 lines changed: 1, context: html, text, full: html, text
    Migrated Neandertal track descriptions from genome-nt.
• src/hg/makeDb/trackDb/urchin/strPur1/trackDb.ra
  • 1.11 lines changed: 16, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/urchin/strPur2/trackDb.ra
  • 1.3 lines changed: 14, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/wallaby/macEug1/trackDb.ra
  • 1.2 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/worm/caePb1/trackDb.ra
  • 1.8 lines changed: 30, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/worm/caePb2/trackDb.ra
  • 1.7 lines changed: 30, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/worm/caeRem2/trackDb.ra
  • 1.10 lines changed: 40, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/worm/caeRem3/trackDb.ra
  • 1.6 lines changed: 27, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/worm/cb1/trackDb.ra
  • 1.24 lines changed: 29, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/worm/ce4/trackDb.ra
  • 1.45 lines changed: 11, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/worm/ce6/trackDb.ra
  • 1.23 lines changed: 28, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/worm/priPac1/trackDb.ra
  • 1.10 lines changed: 37, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/worm/trackDb.ra
  • 1.46 lines changed: 14, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
  • 1.45 lines changed: 20, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/xenTro/xenTro1/trackDb.ra
  • 1.46 lines changed: 29, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/xenTro/xenTro2/trackDb.ra
  • 1.28 lines changed: 29, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/zebrafish/danRer5/trackDb.ra
  • 1.37 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
  • 1.36 lines changed: 6, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDb/zebrafish/danRer6/trackDb.ra
  • 1.11 lines changed: 32, context: html, text, full: html, text
    Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks.
• src/hg/makeDb/trackDb/zebrafish/trackDb.ra
  • 1.81 lines changed: 2, context: html, text, full: html, text
    Changing subTrack to parent.
• src/hg/makeDb/trackDbPatch/trackDbPatch.c
  • 1.5 lines changed: 21, context: html, text, full: html, text
    Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
• src/hg/near/hgNear/association.c
  • 1.14 lines changed: 1, context: html, text, full: html, text
    using htmlEncode via new function hPrintEncodeNonBreak to protect against problems with <>;" in output, problem was recently uncovered by hgNearTest
• src/hg/near/hgNear/colTemplate.c
  • 1.4 lines changed: 11, context: html, text, full: html, text
    using htmlEncode via new function hPrintEncodeNonBreak to protect against problems with <>;" in output, problem was recently uncovered by hgNearTest
• src/hg/near/hgNear/customColumn.c
  • 1.8 lines changed: 3, context: html, text, full: html, text
    using htmlEncode via new function hPrintEncodeNonBreak to protect against problems with <>;" in output, problem was recently uncovered by hgNearTest
• src/hg/near/hgNear/flyBase.c
  • 1.2 lines changed: 1, context: html, text, full: html, text
    using htmlEncode via new function hPrintEncodeNonBreak to protect against problems with <>;" in output, problem was recently uncovered by hgNearTest
• src/hg/near/hgNear/go.c
  • 1.22 lines changed: 1, context: html, text, full: html, text
    using htmlEncode via new function hPrintEncodeNonBreak to protect against problems with <>;" in output, problem was recently uncovered by hgNearTest
• src/hg/near/hgNear/hgNear.c
  • 1.186 lines changed: 6, context: html, text, full: html, text
    using htmlEncode via new function hPrintEncodeNonBreak to protect against problems with <>;" in output, problem was recently uncovered by hgNearTest
• src/hg/near/hgNear/hgNear.h
  • 1.100 lines changed: 3, context: html, text, full: html, text
    using htmlEncode via new function hPrintEncodeNonBreak to protect against problems with <>;" in output, problem was recently uncovered by hgNearTest
• src/hg/near/hgNear/knownGene.c
  • 1.34 lines changed: 1, context: html, text, full: html, text
    using htmlEncode via new function hPrintEncodeNonBreak to protect against problems with <>;" in output, problem was recently uncovered by hgNearTest
• src/hg/oneShot/tdbRewriteViewsToSubtracks1/tdbRewriteViewsToSubtracks1.c
  • 1.2 lines changed: 4, context: html, text, full: html, text
    Making usage statement reflect program name.
• src/hg/oneShot/timeGifPng/timeGifPng.c
  • 1.2 lines changed: 29, context: html, text, full: html, text
    some changes
• src/hg/regulate/regCluster/regCluster.c
  • 1.3 lines changed: 13, context: html, text, full: html, text
    Doing another pass at the regulatory clustering - this time whole genome rather than just chromosome 22.
• src/hg/regulate/regClusterBedExpCfg/regClusterBedExpCfg.c
  • 1.2 lines changed: 91, context: html, text, full: html, text
    Doing another pass at the regulatory clustering - this time whole genome rather than just chromosome 22.
• src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c
  • 1.3 lines changed: 13, context: html, text, full: html, text
    Doing another pass at the regulatory clustering - this time whole genome rather than just chromosome 22.
• src/hg/utils/refreshNamedSessionCustomTracks/refreshSessionCtFilesInner.csh
  • 1.5 lines changed: 1, context: html, text, full: html, text
    fixing error xargs: argument line too long
• src/inc/common.mk
  • 1.79 lines changed: 1, context: html, text, full: html, text
    Put in commented out line that does not have force-warnings-to-errors compiler flag.
• src/inc/maf.h
  • 1.33 lines changed: 1, context: html, text, full: html, text
    strike two at getting name right
  • 1.32 lines changed: 1, context: html, text, full: html, text
    come how got function name wrong in header
  • 1.31 lines changed: 6, context: html, text, full: html, text
    added functions to parse srcDb and src sequence name from mafComp
• src/lib/maf.c
  • 1.44 lines changed: 1, context: html, text, full: html, text
    yet another off by one error in my latest stupidity, wish there were unit tests
  • 1.43 lines changed: 4, context: html, text, full: html, text
    fixed off-by-one error when have a db.chr
  • 1.42 lines changed: 24, context: html, text, full: html, text
    added functions to parse srcDb and src sequence name from mafComp
• src/oneShot/rgbaGfxTest/rgbaGfxTest.c
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Fiddling with spacing.
• src/product/README.install
  • 1.13 lines changed: 1, context: html, text, full: html, text
    adding visiGene
• src/product/ex.hg.conf
  • 1.24 lines changed: 8, context: html, text, full: html, text
    comment out bottleneck setting and add central.cookie information and udcFuse mountPoint
• src/utils/qa/chain.csh
  • 1.33 lines changed: 1, context: html, text, full: html, text
    adding period
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.112 lines changed: 2, context: html, text, full: html, text
    v231 preview

• lines changed: 187446
• files changed: 351