angie: changes by file

branch to review (2010-01-19 to 2010-01-26) v224

• src/hg/hgTables/mainPage.c
  • 1.146 lines changed: 1, context: html, text, full: html, text
    Clarified ENCODE regions label (thanks Kayla/Ann).
• src/hg/hgc/hgc.c
  • 1.1592 lines changed: 8, context: html, text, full: html, text
    pgSjk was not hooked up to doPgSnp, oops! Tweaked wording in pgSnp.
  • 1.1591 lines changed: 96, context: html, text, full: html, text
    gwasCatalog: Added links to dbSNP for snp and, if different, the snp with the risk allele. Look up and display the dbSNP observed alleles, and warn if they are complementary (then the risk allele is ambiguous because strand is not noted.
  • 1.1590 lines changed: 26, context: html, text, full: html, text
    For snp125+, if there is a gwasCatalog table that also contains the SNP, make a link to open the track in hgTracks (like we do for HapMap).
  • 1.1589 lines changed: 68, context: html, text, full: html, text
    Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies).
• src/hg/inc/gwasCatalog.h
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies).
• src/hg/lib/customFactory.c
  • 1.114 lines changed: 1, context: html, text, full: html, text
    Added verbose4 message to add customTrash db tables to the output used by the refresh script.
• src/hg/lib/gwasCatalog.as
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies).
• src/hg/lib/gwasCatalog.c
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies).
• src/hg/lib/gwasCatalog.sql
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies).
• src/hg/lib/hui.c
  • 1.254 lines changed: 1, context: html, text, full: html, text
    baseColorDrawOptDropDown: Similarly to the drop-down labels, use 'base' not 'mRNA' in help link label when there is no coding info.
• src/hg/lib/makefile
  • 1.400 lines changed: 1, context: html, text, full: html, text
    Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies).
• src/hg/lib/pgSnp.c
  • 1.7 lines changed: 5, context: html, text, full: html, text
    Tweaked label of coding changes. If there are no coding changes, suppress messages about coding changes (confused me a bit).
• src/hg/makeDb/doc/hg19.txt
  • 1.73 lines changed: 9, context: html, text, full: html, text
    Added template for Genome Variants (pgSnp) liftOver from hg18 by Belinda.
  • 1.72 lines changed: 18, context: html, text, full: html, text
    Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies).
• src/hg/makeDb/schema/all.joiner
  • 1.766 lines changed: 3, context: html, text, full: html, text
    Added gwasCatalog.
• src/hg/makeDb/trackDb/README
  • 1.97 lines changed: 17, context: html, text, full: html, text
    Added 'type bam' description.
• src/hg/makeDb/trackDb/tagTypes.tab
  • 1.8 lines changed: 2, context: html, text, full: html, text
    Adding snpTable and snpVersion (and url, urlLabel) to gwasCatalog.
• src/hg/makeDb/trackDb/human/gwasCatalog.html
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies).
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.498 lines changed: 4, context: html, text, full: html, text
    Adding snpTable and snpVersion (and url, urlLabel) to gwasCatalog.
  • 1.496 lines changed: 1, context: html, text, full: html, text
    Bumped up gwasCatalog's searchPriority, Jim's request.
  • 1.495 lines changed: 1, context: html, text, full: html, text
    Change gwasCatalog color from blue to green (neighboring tracks are blue).
  • 1.494 lines changed: 17, context: html, text, full: html, text
    Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies).
• src/hg/makeDb/trackDb/human/hg18/pgSnp.html
  • 1.12 lines changed: 2, context: html, text, full: html, text
    Oops, forgot to use &lt; instead of bare < .
  • 1.11 lines changed: 3, context: html, text, full: html, text
    Corrections: Venter and Illumina's Yoruban variants are not just single-base. Thanks Mark!
• src/hg/makeDb/trackDb/human/hg19/pgSnp.html
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Belinda's liftOver'd personal genome variants.
• src/hg/utils/refreshNamedSessionCustomTracks/refreshSessionCtFilesInner.csh
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Adding -atime=123 option to refreshNamedSessionCustomTracks, so we will no longer refresh files in sessions that have not been accessed in >4 months.