mikep: changes by commit

branch to review (2009-05-26 to 2009-06-02) v207

• showing diffBases for Helicos until we can find an alignment format
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.311 - lines changed: 5, context: html, text, full: html, text
• turn off the base display until we have a better visualization
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.312 - lines changed: 4, context: html, text, full: html, text
• rename view to FiltTransfrags to ensure MySQL tablenames shorter than 65
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.318 - lines changed: 47, context: html, text, full: html, text
• fix up FilteredRawSignal View name to be shorter FiltRawSignal for mysql table names
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.319 - lines changed: 48, context: html, text, full: html, text
• shortened view names
  • src/hg/encode/DAFs/AffyRnaChip.daf 1.5 - lines changed: 2, context: html, text, full: html, text
• adding 4 new AffyRnaChip submissions, removing old duplicated metadata settings, adding a missing metadata line
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.321 - lines changed: 590, context: html, text, full: html, text
• dont print the full record if all the fields are already nicely formatted above
  • src/hg/hgc/bigBedClick.c 1.4 - lines changed: 1, context: html, text, full: html, text
• show seq1,seq2 columns (non-standard bed cols 7+8) for pairedTagAlign
  • src/hg/hgc/hgc.c 1.1547 - lines changed: 4, context: html, text, full: html, text
• show seq1,seq2 columns (non-standard bed cols 7+8) for pairedTagAlign. This is not very nice way to deal with it, asking Jim for other suggestion.
  • src/hg/hgc/bigBedClick.c 1.5 - lines changed: 13, context: html, text, full: html, text
• removign /cluster/hive even from comment in case it causes confusion
  • src/utils/qa/weeklybld/buildCvsReports.csh 1.22 - lines changed: 1, context: html, text, full: html, text
• make colorByStrand independent of baseColor
  • src/hg/hgTracks/bedTrack.c 1.12 - lines changed: 4, context: html, text, full: html, text
• make colorByStrand work for ordinary beds (item is a bed) and for sequences where basecoloring is done (item is a linkedFeature)
  • src/hg/hgTracks/bedTrack.c 1.13 - lines changed: 33, context: html, text, full: html, text
• choose a contrasting color for tick marks when drawgin differnt bases
  • src/hg/hgTracks/cds.c 1.98 - lines changed: 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/README 1.74 - lines changed: 5, context: html, text, full: html, text
• adding option to replace default 'red' tickmarks with contrasting or lighter color ones similar to the color in zoomed in base view
  • src/hg/hgTracks/cds.c 1.99 - lines changed: 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/README 1.75 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.323 - lines changed: 20, context: html, text, full: html, text
• no, we do not, the type of a track is its type no need to consult parent
  • src/hg/hgTables/joining.c 1.55 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTables/wiggle.c 1.74 - lines changed: 1, context: html, text, full: html, text
• disable JavaScript on the rest of the pages
  • java/src/edu/ucsc/genome/qa/cgiCheck/TrackCheck.java 1.13 - lines changed: 4, context: html, text, full: html, text
  • java/src/edu/ucsc/genome/qa/lib/HgTracks.java 1.17 - lines changed: 9, context: html, text, full: html, text
• v208 preview
  • src/utils/qa/weeklybld/buildEnv.csh 1.61 - lines changed: 2, context: html, text, full: html, text