angie: changes by file

branch to review (2009-03-10 to 2009-03-17) v202

• src/hg/checkTableCoords/tests/input/pslCTCBad.psl
  • 1.2 lines changed: 0, context: html, text, full: html, text
    Fixed formatting error (too many tabs) that was tolerated when hgLoadPsl wrote its own .tab file for loading but caused trouble when hgLoadPsl (with -nobin and -noSort) sent this file directly to mysql.
• src/hg/hgSession/hgSession.c
  • 1.49 lines changed: 3, context: html, text, full: html, text
    Added Browser and Email links after session-update message - thanks b0b for the suggestion!
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.478 lines changed: 1, context: html, text, full: html, text
    hapmapSnpsUi: incomplete html found by Jim in code review.
• src/hg/hgTracks/simpleTracks.c
  • 1.69 lines changed: 1, context: html, text, full: html, text
    Registered pgSnpHgwdev (Belinda's Genome Variants subtracks that should remain on hgwdev for now.
• src/hg/hgc/hgc.c
  • 1.1518 lines changed: 32, context: html, text, full: html, text
    Extra vertical whitespace between alt. pcr matches as suggested by Brooke. For HapMap SNPs (Phase III), show average of populations' allele frequencies instead of sum of all individual alleles.
• src/hg/makeDb/doc/droMoj2.txt
  • 1.4 lines changed: 11, context: html, text, full: html, text
    LiftOver to dm3 for genome list q.
• src/hg/makeDb/doc/hg17.txt
  • 1.120 lines changed: 9, context: html, text, full: html, text
    Updated DGV (v7).
• src/hg/makeDb/doc/hg18.txt
  • 1.356 lines changed: 21, context: html, text, full: html, text
    Fixed coords of hgdpHzyBantu and reloaded.
  • 1.355 lines changed: 11, context: html, text, full: html, text
    Updated DGV (v7).
  • 1.354 lines changed: 110, context: html, text, full: html, text
    Adding sections for Genome Variants subtracks loaded by Belinda.
• src/hg/makeDb/hgLoadBed/hgLoadBed.c
  • 1.67 lines changed: 14, context: html, text, full: html, text
    Restoring option -allowStartEqualEnd which I shouldn't have removed in 1.52 (thanks Kate). SNPs and other tracks with valid 0-length items like insertion points will have to use -allowStartEqualEnd, but most tracks will get the appropriate level of checking b y default.
• src/hg/makeDb/hgLoadPsl/hgLoadPsl.c
  • 1.34 lines changed: 54, context: html, text, full: html, text
    Sort output by target coords unless -noSort is specified. Thanks MarkD for the idea to pipe output to sort!
• src/hg/makeDb/schema/all.joiner
  • 1.700 lines changed: 6, context: html, text, full: html, text
    Added Genome Variants tables to tablesIgnored.
• src/hg/makeDb/trackDb/human/hgdpIhs.html
  • 1.4 lines changed: 11, context: html, text, full: html, text
    Added more descriptive info from ref's and added links to source code tars from Joe Pickrell.
• src/hg/makeDb/trackDb/human/hgdpXpehh.html
  • 1.3 lines changed: 9, context: html, text, full: html, text
    Added more descriptive info from ref's and added links to source code tars from Joe Pickrell.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.442 lines changed: 1, context: html, text, full: html, text
    Removed the alpha from hgdpHzyBantu -- coords adjusted, looks good now.
  • 1.441 lines changed: 3, context: html, text, full: html, text
    Added release alpha setting to subtrack hgdpHzyBantu because it seems to be in a different format than the others. Updated DGV's dataVersion to v7.
• src/hg/makeDb/trackDb/human/hg17/hapmapSnps.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Added missing <P>.
• src/hg/makeDb/trackDb/human/hg18/pgSnp.html
  • 1.7 lines changed: 56, context: html, text, full: html, text
    Split off the unreleaseable subtracks of pgSnp (Genome Variants) into a new composite track, pgSnpHgwdev. More polishing of pgSnp.html in preparation for release.
• src/hg/makeDb/trackDb/human/hg18/pgSnpHgwdev.html
  • 1.1 lines changed: 61, context: html, text, full: html, text
    Split off the unreleaseable subtracks of pgSnp (Genome Variants) into a new composite track, pgSnpHgwdev. More polishing of pgSnp.html in preparation for release.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.382 lines changed: 22, context: html, text, full: html, text
    Split off the unreleaseable subtracks of pgSnp (Genome Variants) into a new composite track, pgSnpHgwdev. More polishing of pgSnp.html in preparation for release.
• src/hg/qa/apacheMonitor.c
  • 1.15 lines changed: 4, context: html, text, full: html, text
    Always show up to 20 most recent error 500's.