mikep: changes by commit

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

• 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/hui.c 1.197 - lines changed: 3, 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/bedTrack.c 1.7 - lines changed: 71, context: html, text, full: html, text
  • src/hg/hgTracks/cds.c 1.95 - lines changed: 32, context: html, text, full: html, text
  • src/hg/hgTracks/cds.h 1.22 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c 1.81 - 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/asObj.c 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTables/bedList.c 1.68 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTables/bigBed.c 1.9 - lines changed: 5, context: html, text, full: html, text
  • src/hg/hgTables/bigWig.c 1.5 - lines changed: 2, context: html, text, full: html, text
  • src/hg/hgTables/compositeTrack.c 1.17 - lines changed: 27, context: html, text, full: html, text
  • src/hg/hgTables/correlate.c 1.77 - lines changed: 3, context: html, text, full: html, text
  • src/hg/hgTables/custom.c 1.41 - lines changed: 8, context: html, text, full: html, text
  • src/hg/hgTables/filterFields.c 1.75 - lines changed: 6, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.c 1.186 - lines changed: 13, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.h 1.138 - lines changed: 18, context: html, text, full: html, text
  • src/hg/hgTables/intersect.c 1.51 - lines changed: 2, context: html, text, full: html, text
  • src/hg/hgTables/joining.c 1.54 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTables/maf.c 1.17 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTables/mainPage.c 1.144 - lines changed: 3, context: html, text, full: html, text
  • src/hg/hgTables/microarrayTables.c 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTables/rangeHistogram.c 1.6 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTables/schema.c 1.60 - lines changed: 4, context: html, text, full: html, text
  • src/hg/hgTables/seqOut.c 1.23 - lines changed: 2, context: html, text, full: html, text
  • src/hg/hgTables/sumStats.c 1.28 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTables/wiggle.c 1.73 - lines changed: 9, context: html, text, full: html, text
  • src/hg/inc/hdb.h 1.167 - lines changed: 28, context: html, text, full: html, text
  • src/hg/lib/hdb.c 1.403 - lines changed: 61, context: html, text, full: html, text
• Show bases different to teh genome in the RIKEN tagAligns
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.303 - lines changed: 44, 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/README 1.71 - lines changed: 14, context: html, text, full: html, text
• error with the Riken Polysome data, should be PolyA-
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.304 - lines changed: 18, 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/hgTracks/bedTrack.c 1.8 - lines changed: 30, context: html, text, full: html, text
  • src/hg/inc/trackDb.h 1.49 - lines changed: 4, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c 1.66 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/README 1.72 - lines changed: 4, context: html, text, full: html, text
• first cut of RIKEN colorByStrand settings
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.306 - lines changed: 11, context: html, text, full: html, text
• getting rid of offending colon cancer
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.307 - lines changed: 11, context: html, text, full: html, text
• get rid of colon between +/- strands and split on space, by popular demand
  • src/hg/hgTracks/bedTrack.c 1.9 - lines changed: 2, context: html, text, full: html, text
• Added pairedTagAlign baseColor option controlled by 'seq1Seq2' option to baseColorUseSequence
  • src/hg/hgTracks/bedTrack.c 1.10 - lines changed: 87, context: html, text, full: html, text
  • src/hg/hgTracks/cds.c 1.96 - lines changed: 6, context: html, text, full: html, text
  • src/hg/lib/hui.c 1.203 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/README 1.73 - lines changed: 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.310 - lines changed: 48, context: html, text, full: html, text
• forgot or
  • src/hg/lib/hui.c 1.204 - lines changed: 1, context: html, text, full: html, text
• simplify code and add warning about assuming seq1,seq2 are in row[6] and row[7] respectively
  • src/hg/hgTracks/bedTrack.c 1.11 - lines changed: 18, context: html, text, full: html, text
• v207 final build
  • src/utils/qa/weeklybld/buildEnv.csh 1.60 - lines changed: 3, context: html, text, full: html, text
• "New version number v207"
  • src/hg/inc/versionInfo.h 1.147 - lines changed: 1, context: html, text, full: html, text