angie: changes by commit

branch to review (2009-02-09 to 2009-02-17) v200

• Use hg.conf settings to determine GMT executable paths and enable/disable images, instead of hIsPrivateHost.
  • src/hg/hgc/hgdpClick.c 1.5 - lines changed: 45, context: html, text, full: html, text
• Another addition from Graham Coop in Methods, and another reference from John Novembre.
  • src/hg/makeDb/trackDb/human/hgdpGeo.html 1.5 - lines changed: 14, context: html, text, full: html, text
• Made bdtnpChipper full by Mark Biggin's request.
  • src/hg/makeDb/trackDb/drosophila/trackDb.ra 1.74 - lines changed: 1, context: html, text, full: html, text
• Per-SNP geographic map data and scripts from Human Genome Diversity Project.
  • src/hg/makeDb/doc/hgdpGeo.txt 1.1 - lines changed: 127, context: html, text, full: html, text
• Performance fix for tableExists: use sqlTableWildExists only when table name has a wildcard, because in large dbs like hg18, sqlTableWildExists is ~100x slower than sqlTableExists (0.090s --> 0.000s). When joining through gbCdnaInfo, we may call tableExists 255 times to find a path to tissue.name.
  • src/hg/lib/joiner.c 1.28 - lines changed: 3, context: html, text, full: html, text
• Added alpha and beta release settings for komp, which is having its labels changed from KOMP to IKMC (Int'l Knockout Mouse Consortium).
  • src/hg/makeDb/trackDb/mouse/trackDb.ra 1.152 - lines changed: 16, context: html, text, full: html, text
• Expanded to describe the International Knockout Mouse Consortium of which KOMP is part.
  • src/hg/makeDb/trackDb/mouse/komp.html 1.3 - lines changed: 56, context: html, text, full: html, text
• Added 4 new tracks from the HGDP Selection Browser: FST and Per-continent heterozygosity, iHS and XP-EHH.
  • src/hg/makeDb/trackDb/human/hgdpFst.html 1.1 - lines changed: 88, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hgdpHzy.html 1.1 - lines changed: 58, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hgdpIhs.html 1.1 - lines changed: 72, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hgdpXpehh.html 1.1 - lines changed: 66, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra 1.436 - lines changed: 178, context: html, text, full: html, text
• Added continent colors to hgdpHzy, hgdpIhs and hgdpXpehh to match HGDP Selection Browser coloring.
  • src/hg/makeDb/trackDb/human/trackDb.ra 1.437 - lines changed: 21, context: html, text, full: html, text
• pgSnp: label tweaks at David's request.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.370 - lines changed: 18, context: html, text, full: html, text
• pgSnp: a few more label tweaks for consistency.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.371 - lines changed: 4, context: html, text, full: html, text