angie: changes by commit

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

• 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).
  • src/hg/hgc/hgc.c 1.1590 - lines changed: 26, context: html, text, full: html, text
• Change gwasCatalog color from blue to green (neighboring tracks are blue).
  • src/hg/makeDb/trackDb/human/trackDb.ra 1.495 - 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/customFactory.c 1.114 - lines changed: 1, context: html, text, full: html, text
• Bumped up gwasCatalog's searchPriority, Jim's request.
  • src/hg/makeDb/trackDb/human/trackDb.ra 1.496 - lines changed: 1, 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/hg18/pgSnp.html 1.11 - lines changed: 3, context: html, text, full: html, text
• Oops, forgot to use &lt; instead of bare < .
  • src/hg/makeDb/trackDb/human/hg18/pgSnp.html 1.12 - lines changed: 2, context: html, text, full: html, text
• Belinda's liftOver'd personal genome variants.
  • src/hg/makeDb/trackDb/human/hg19/pgSnp.html 1.1 - lines changed: 0, context: html, text, full: html, text
• Added 'type bam' description.
  • src/hg/makeDb/trackDb/README 1.97 - lines changed: 17, 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/hui.c 1.254 - lines changed: 1, context: html, text, full: html, text
• Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies).
  • src/hg/hgc/hgc.c 1.1589 - lines changed: 68, context: html, text, full: html, text
  • src/hg/inc/gwasCatalog.h 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/lib/gwasCatalog.as 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/lib/gwasCatalog.c 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/lib/gwasCatalog.sql 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/lib/makefile 1.400 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt 1.72 - lines changed: 18, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/gwasCatalog.html 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra 1.494 - lines changed: 17, 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.
  • src/hg/utils/refreshNamedSessionCustomTracks/refreshSessionCtFilesInner.csh 1.4 - lines changed: 1, 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.
  • src/hg/hgc/hgc.c 1.1591 - lines changed: 96, context: html, text, full: html, text
• Adding snpTable and snpVersion (and url, urlLabel) to gwasCatalog.
  • src/hg/makeDb/trackDb/human/trackDb.ra 1.498 - lines changed: 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab 1.8 - lines changed: 2, context: html, text, full: html, text
• pgSjk was not hooked up to doPgSnp, oops! Tweaked wording in pgSnp.
  • src/hg/hgc/hgc.c 1.1592 - lines changed: 8, 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/lib/pgSnp.c 1.7 - lines changed: 5, context: html, text, full: html, text
• Added gwasCatalog.
  • src/hg/makeDb/schema/all.joiner 1.766 - lines changed: 3, context: html, text, full: html, text
• Added template for Genome Variants (pgSnp) liftOver from hg18 by Belinda.
  • src/hg/makeDb/doc/hg19.txt 1.73 - lines changed: 9, context: html, text, full: html, text
• Clarified ENCODE regions label (thanks Kayla/Ann).
  • src/hg/hgTables/mainPage.c 1.146 - lines changed: 1, context: html, text, full: html, text