angie: changes by commit

branch to review (2009-02-24 to 2009-03-03) v201

• User+local request: show the primer boundaries in hgPcr results.
  • src/hg/hgTracks/hgTracks.c 1.1555 - lines changed: 3, context: html, text, full: html, text
• Correction from Joe Pickrell.
  • src/hg/makeDb/trackDb/human/hgdpIhs.html 1.2 - lines changed: 1, context: html, text, full: html, text
• Make canonicalRangeExp accept negative start coord -- hgTracks will clip to 0.
  • src/hg/lib/hgFind.c 1.218 - lines changed: 1, context: html, text, full: html, text
• Use sqlConnectRemote instead of hAllocConn (host was being ignored). Reuse one conn instead of realloc'ing in every function. Bump up the verbosity level of most messages, to make the error counts stand out.
  • src/hg/qa/apacheMonitor.c 1.13 - lines changed: 57, context: html, text, full: html, text
• Made dbIsFound a global so there's no need to set it again after doMiddle sets it.
  • src/hg/hgc/hgc.c 1.1511 - lines changed: 7, context: html, text, full: html, text
• Added sqlSetParanoid; complain about failed MayConnect only if paranoidness is on (the only time we really should complain is when trying to get to the central database.
  • src/hg/inc/jksql.h 1.81 - lines changed: 3, context: html, text, full: html, text
  • src/hg/lib/jksql.c 1.128 - lines changed: 9, context: html, text, full: html, text
• Made hgSeqChromSize more concise, and took out a redundant call to it (chromSize is passed down instead).
  • src/hg/lib/hgSeq.c 1.39 - lines changed: 20, context: html, text, full: html, text
• Use the new sqlSetParanoid to enable extra stderr message if we fail to connect to the central database.
  • src/hg/lib/hdb.c 1.396 - lines changed: 2, context: html, text, full: html, text
• Some fields can be null -- added checks.
  • src/hg/qa/apacheMonitor.c 1.14 - lines changed: 5, context: html, text, full: html, text
• Added hgdpHzyBantu and changed 'Africa' to 'Bantu' in hgdpIhs and hgdpXpehh. Added hapmapSnps* for 7 new populations in HapMap Phase III.
  • src/hg/makeDb/trackDb/human/trackDb.ra 1.439 - lines changed: 69, context: html, text, full: html, text
• Correction: only Bantu populations (not all African pops) were used to calculate iHS and XP-EHH.
  • src/hg/makeDb/trackDb/human/hgdpHzy.html 1.2 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hgdpIhs.html 1.3 - lines changed: 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hgdpXpehh.html 1.2 - lines changed: 9, context: html, text, full: html, text
• Fixed hgdpHzy subtrack priorities (forgot they're int not float).
  • src/hg/makeDb/trackDb/human/trackDb.ra 1.440 - lines changed: 7, context: html, text, full: html, text
• Refactored hapmapSnps code to support both phase II (4 populations) and phase III (11 populations) SNPs.
  • src/hg/hgc/hgc.c 1.1512 - lines changed: 247, context: html, text, full: html, text
• Updated hapmapSnpsUi to handle HapMap phase III (11 populations).
  • src/hg/hgTrackUi/hgTrackUi.c 1.474 - lines changed: 151, context: html, text, full: html, text
• Added global vars: lists of population codes and ortho-species for HapMap Phase II and III.
  • src/hg/lib/hapmapSnps.c 1.4 - lines changed: 5, context: html, text, full: html, text
• Added some new #defines for the HapMap Phase III updates to hgc, hgTrackUi and hgTracks.
  • src/hg/inc/hapmapSnps.h 1.6 - lines changed: 31, context: html, text, full: html, text