Commits for angie

v239_base to v240_preview (2010-08-31 to 2010-09-07) v240

• Description by Mark Biggin w/minor formatting/wording tweaks.
  • src/hg/makeDb/trackDb/drosophila/bdtnpDnase.html - lines changed 57, context: html, text, full: html, text
• Small tweaks based on Results section of manuscript.
  • src/hg/makeDb/trackDb/drosophila/bdtnpDnase.html - lines changed 7, context: html, text, full: html, text
• Added brief mention of new subtracks and the new reference for them.
  • src/hg/makeDb/trackDb/drosophila/bdtnpChipper.html - lines changed 15, context: html, text, full: html, text
• Use complete gene names for all factor labels, not just the latter half of them -- don't know why I didn't before.
  • src/hg/makeDb/trackDb/drosophila/trackDb.ra - lines changed 1, context: html, text, full: html, text
• Fix to addBamPaired for code that detects unpaired items for gray mode -- Brian found that it was missing most of them, doh!
  • src/hg/hgTracks/bamTrack.c - lines changed 4, context: html, text, full: html, text
• Performance fix for drawScaledBoxSampleWithText: fixed unnecessary O(N^2) loop condition -- now it will iterate no more than (winEnd-winStart), at base zoom.
  • src/hg/hgTracks/cds.c - lines changed 8, context: html, text, full: html, text
• GWAS catalog data update.
  • src/hg/makeDb/doc/hg18.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 3, context: html, text, full: html, text
• Barely started gathering data for fosEndPairs. checking in so I can switch branches.
  • src/hg/makeDb/doc/hg19.txt - lines changed 13, context: html, text, full: html, text
• More liftOver'd BDTNP data.
  • src/hg/makeDb/doc/dm3.txt - lines changed 45, context: html, text, full: html, text
• Geez, got my min and max swapped in f808c044.
  • src/hg/hgTracks/cds.c - lines changed 4, context: html, text, full: html, text
• Fix snp131Clinical's missing-func item, which is still in snp131.bed.
  • src/hg/makeDb/doc/hg19.txt - lines changed 4, context: html, text, full: html, text
• Disable 'view table schema' link when setting 'tableBrowser off' is present.
  • src/hg/lib/hui.c - lines changed 4, context: html, text, full: html, text
• Redmine #717: obey tableBrowser off setting in 'selected fields from primary and related tables' page (thanks Brooke) and table schema 'Connected Tables and Joining Fields'.
  • src/hg/hgTables/filterFields.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.h - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTables/mainPage.c - lines changed 37, context: html, text, full: html, text
  • src/hg/hgTables/schema.c - lines changed 2, context: html, text, full: html, text
• Redmine #717: Plugging one more leak that needs to check accessControlDenied.
  • src/hg/hgTables/hgTables.c - lines changed 2, context: html, text, full: html, text
• Adding html override for bdtnpChipper until release of new data.
  • src/hg/makeDb/trackDb/drosophila/bdtnpChipperOld.html - lines changed 189, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/dm2/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/dm3/trackDb.ra - lines changed 8, context: html, text, full: html, text