angie: changes by file

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

• src/hg/hgc/hgdpClick.c
  • 1.5 lines changed: 45, context: html, text, full: html, text
    Use hg.conf settings to determine GMT executable paths and enable/disable images, instead of hIsPrivateHost.
• src/hg/lib/joiner.c
  • 1.28 lines changed: 3, 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/makeDb/doc/hgdpGeo.txt
  • 1.1 lines changed: 127, context: html, text, full: html, text
    Per-SNP geographic map data and scripts from Human Genome Diversity Project.
• src/hg/makeDb/trackDb/drosophila/trackDb.ra
  • 1.74 lines changed: 1, context: html, text, full: html, text
    Made bdtnpChipper full by Mark Biggin's request.
• src/hg/makeDb/trackDb/human/hgdpFst.html
  • 1.1 lines changed: 88, 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/hgdpGeo.html
  • 1.5 lines changed: 14, context: html, text, full: html, text
    Another addition from Graham Coop in Methods, and another reference from John Novembre.
• src/hg/makeDb/trackDb/human/hgdpHzy.html
  • 1.1 lines changed: 58, 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/hgdpIhs.html
  • 1.1 lines changed: 72, 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/hgdpXpehh.html
  • 1.1 lines changed: 66, 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/trackDb.ra
  • 1.437 lines changed: 21, context: html, text, full: html, text
    Added continent colors to hgdpHzy, hgdpIhs and hgdpXpehh to match HGDP Selection Browser coloring.
  • 1.436 lines changed: 178, 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/hg18/trackDb.ra
  • 1.371 lines changed: 4, context: html, text, full: html, text
    pgSnp: a few more label tweaks for consistency.
  • 1.370 lines changed: 18, context: html, text, full: html, text
    pgSnp: label tweaks at David's request.
• src/hg/makeDb/trackDb/mouse/komp.html
  • 1.3 lines changed: 56, context: html, text, full: html, text
    Expanded to describe the International Knockout Mouse Consortium of which KOMP is part.
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • 1.152 lines changed: 16, 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).