mikep: changes by file

review to branch (2009-05-19 to 2009-05-26) v207

• src/hg/hgTables/asObj.c
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/bedList.c
  • 1.68 lines changed: 1, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/bigBed.c
  • 1.9 lines changed: 5, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/bigWig.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/compositeTrack.c
  • 1.17 lines changed: 27, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/correlate.c
  • 1.77 lines changed: 3, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/custom.c
  • 1.41 lines changed: 8, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/filterFields.c
  • 1.75 lines changed: 6, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/hgTables.c
  • 1.186 lines changed: 13, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/hgTables.h
  • 1.138 lines changed: 18, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/intersect.c
  • 1.51 lines changed: 2, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/joining.c
  • 1.54 lines changed: 1, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/maf.c
  • 1.17 lines changed: 1, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/mainPage.c
  • 1.144 lines changed: 3, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/microarrayTables.c
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/rangeHistogram.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/schema.c
  • 1.60 lines changed: 4, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/seqOut.c
  • 1.23 lines changed: 2, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/sumStats.c
  • 1.28 lines changed: 1, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/wiggle.c
  • 1.73 lines changed: 9, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTracks/bedTrack.c
  • 1.11 lines changed: 18, context: html, text, full: html, text
    simplify code and add warning about assuming seq1,seq2 are in row[6] and row[7] respectively
  • 1.10 lines changed: 87, context: html, text, full: html, text
    Added pairedTagAlign baseColor option controlled by 'seq1Seq2' option to baseColorUseSequence
  • 1.9 lines changed: 2, context: html, text, full: html, text
    get rid of colon between +/- strands and split on space, by popular demand
  • 1.8 lines changed: 30, context: html, text, full: html, text
    added 'colorByStrand' option which specifies a + and - strand color to override the main 'color', currently works for bed/bigBed tracks which have base coloring
  • 1.7 lines changed: 71, context: html, text, full: html, text
    display sequence or sequence different to the genome using a bed or bigBed which has the sequence in the name (eg tagAlign) in a similar manner to PSL files (by loading the BED as a linkedFeature like a PSL)
• src/hg/hgTracks/cds.c
  • 1.96 lines changed: 6, context: html, text, full: html, text
    Added pairedTagAlign baseColor option controlled by 'seq1Seq2' option to baseColorUseSequence
  • 1.95 lines changed: 32, context: html, text, full: html, text
    display sequence or sequence different to the genome using a bed or bigBed which has the sequence in the name (eg tagAlign) in a similar manner to PSL files (by loading the BED as a linkedFeature like a PSL)
• src/hg/hgTracks/cds.h
  • 1.22 lines changed: 1, context: html, text, full: html, text
    display sequence or sequence different to the genome using a bed or bigBed which has the sequence in the name (eg tagAlign) in a similar manner to PSL files (by loading the BED as a linkedFeature like a PSL)
• src/hg/hgTracks/simpleTracks.c
  • 1.81 lines changed: 1, context: html, text, full: html, text
    display sequence or sequence different to the genome using a bed or bigBed which has the sequence in the name (eg tagAlign) in a similar manner to PSL files (by loading the BED as a linkedFeature like a PSL)
• src/hg/inc/hdb.h
  • 1.167 lines changed: 28, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/inc/trackDb.h
  • 1.49 lines changed: 4, context: html, text, full: html, text
    added 'colorByStrand' option which specifies a + and - strand color to override the main 'color', currently works for bed/bigBed tracks which have base coloring
• src/hg/inc/versionInfo.h
  • 1.147 lines changed: 1, context: html, text, full: html, text
    "New version number v207"
• src/hg/lib/hdb.c
  • 1.403 lines changed: 61, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/lib/hui.c
  • 1.204 lines changed: 1, context: html, text, full: html, text
    forgot or
  • 1.203 lines changed: 3, context: html, text, full: html, text
    Added pairedTagAlign baseColor option controlled by 'seq1Seq2' option to baseColorUseSequence
  • 1.197 lines changed: 3, context: html, text, full: html, text
    adding a new trackDb.ra option to get the sequence from the name column of a bed file (plus fixing a logic flaw in case an invalid setting was chosen)
• src/hg/lib/trackDbCustom.c
  • 1.66 lines changed: 6, context: html, text, full: html, text
    added 'colorByStrand' option which specifies a + and - strand color to override the main 'color', currently works for bed/bigBed tracks which have base coloring
• src/hg/makeDb/trackDb/README
  • 1.73 lines changed: 16, context: html, text, full: html, text
    Added pairedTagAlign baseColor option controlled by 'seq1Seq2' option to baseColorUseSequence
  • 1.72 lines changed: 4, context: html, text, full: html, text
    added 'colorByStrand' option which specifies a + and - strand color to override the main 'color', currently works for bed/bigBed tracks which have base coloring
  • 1.71 lines changed: 14, context: html, text, full: html, text
    adding new baseColor options to get the sequence from the name field (eg tagAlign tracks), and updated the track type list
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.310 lines changed: 48, context: html, text, full: html, text
    Added pairedTagAlign baseColor option controlled by 'seq1Seq2' option to baseColorUseSequence
  • 1.307 lines changed: 11, context: html, text, full: html, text
    getting rid of offending colon cancer
  • 1.306 lines changed: 11, context: html, text, full: html, text
    first cut of RIKEN colorByStrand settings
  • 1.304 lines changed: 18, context: html, text, full: html, text
    error with the Riken Polysome data, should be PolyA-
  • 1.303 lines changed: 44, context: html, text, full: html, text
    Show bases different to teh genome in the RIKEN tagAligns
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.60 lines changed: 3, context: html, text, full: html, text
    v207 final build