angie: changes by commit

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

• Registered pgSnpHgwdev (Belinda's Genome Variants subtracks that should remain on hgwdev for now.
  • src/hg/hgTracks/simpleTracks.c 1.69 - lines changed: 1, 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/pgSnp.html 1.7 - lines changed: 56, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/pgSnpHgwdev.html 1.1 - lines changed: 61, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.382 - lines changed: 22, context: html, text, full: html, text
• hapmapSnpsUi: incomplete html found by Jim in code review.
  • src/hg/hgTrackUi/hgTrackUi.c 1.478 - lines changed: 1, context: html, text, full: html, text
• Added Genome Variants tables to tablesIgnored.
  • src/hg/makeDb/schema/all.joiner 1.700 - lines changed: 6, context: html, text, full: html, text
• Adding sections for Genome Variants subtracks loaded by Belinda.
  • src/hg/makeDb/doc/hg18.txt 1.354 - lines changed: 110, 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/trackDb.ra 1.441 - lines changed: 3, context: html, text, full: html, text
• Updated DGV (v7).
  • src/hg/makeDb/doc/hg17.txt 1.120 - lines changed: 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg18.txt 1.355 - lines changed: 11, 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/hgLoadBed/hgLoadBed.c 1.67 - lines changed: 14, 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/hgLoadPsl/hgLoadPsl.c 1.34 - lines changed: 54, context: html, text, full: html, text
• Removed the alpha from hgdpHzyBantu -- coords adjusted, looks good now.
  • src/hg/makeDb/trackDb/human/trackDb.ra 1.442 - lines changed: 1, context: html, text, full: html, text
• Fixed coords of hgdpHzyBantu and reloaded.
  • src/hg/makeDb/doc/hg18.txt 1.356 - lines changed: 21, 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/hgdpIhs.html 1.4 - lines changed: 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hgdpXpehh.html 1.3 - lines changed: 9, context: html, text, full: html, text
• Added Browser and Email links after session-update message - thanks b0b for the suggestion!
  • src/hg/hgSession/hgSession.c 1.49 - lines changed: 3, 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/hgc/hgc.c 1.1518 - lines changed: 32, context: html, text, full: html, text
• LiftOver to dm3 for genome list q.
  • src/hg/makeDb/doc/droMoj2.txt 1.4 - lines changed: 11, 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/checkTableCoords/tests/input/pslCTCBad.psl 1.2 - lines changed: 0, context: html, text, full: html, text
• Added missing <P>.
  • src/hg/makeDb/trackDb/human/hg17/hapmapSnps.html 1.3 - lines changed: 1, context: html, text, full: html, text
• Always show up to 20 most recent error 500's.
  • src/hg/qa/apacheMonitor.c 1.15 - lines changed: 4, context: html, text, full: html, text