angie: changes by file

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

• src/hg/hgTrackUi/hgTrackUi.c
  • 1.474 lines changed: 151, context: html, text, full: html, text
    Updated hapmapSnpsUi to handle HapMap phase III (11 populations).
• src/hg/hgTracks/hgTracks.c
  • 1.1555 lines changed: 3, context: html, text, full: html, text
    User+local request: show the primer boundaries in hgPcr results.
• src/hg/hgc/hgc.c
  • 1.1512 lines changed: 247, context: html, text, full: html, text
    Refactored hapmapSnps code to support both phase II (4 populations) and phase III (11 populations) SNPs.
  • 1.1511 lines changed: 7, 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/inc/hapmapSnps.h
  • 1.6 lines changed: 31, context: html, text, full: html, text
    Added some new #defines for the HapMap Phase III updates to hgc, hgTrackUi and hgTracks.
• src/hg/inc/jksql.h
  • 1.81 lines changed: 3, 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/lib/hapmapSnps.c
  • 1.4 lines changed: 5, 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/hdb.c
  • 1.396 lines changed: 2, 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/hgFind.c
  • 1.218 lines changed: 1, context: html, text, full: html, text
    Make canonicalRangeExp accept negative start coord -- hgTracks will clip to 0.
• src/hg/lib/hgSeq.c
  • 1.39 lines changed: 20, 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/jksql.c
  • 1.128 lines changed: 9, 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/makeDb/trackDb/human/hgdpHzy.html
  • 1.2 lines changed: 6, 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/hgdpIhs.html
  • 1.3 lines changed: 11, context: html, text, full: html, text
    Correction: only Bantu populations (not all African pops) were used to calculate iHS and XP-EHH.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Correction from Joe Pickrell.
• src/hg/makeDb/trackDb/human/hgdpXpehh.html
  • 1.2 lines changed: 9, 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/trackDb.ra
  • 1.440 lines changed: 7, context: html, text, full: html, text
    Fixed hgdpHzy subtrack priorities (forgot they're int not float).
  • 1.439 lines changed: 69, 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/qa/apacheMonitor.c
  • 1.14 lines changed: 5, context: html, text, full: html, text
    Some fields can be null -- added checks.
  • 1.13 lines changed: 57, 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.