File Changes for hiram

v264_preview to v264_preview2 (2012-02-21 to 2012-02-28) v264

• src/hg/hgGene/hgGeneData/otherOrgs.ra
  • lines changed 3, context: html, text, full: html, text
    changing rn4 rules
  • lines changed 1, context: html, text, full: html, text
    add a geneUrl rule to the Rat section
  • lines changed 1, context: html, text, full: html, text
    no otherIdSql needed, the RGD id is ready to go as is
• src/hg/htdocs/images/2.jpg
  • lines changed 0, context: html, text, full: html, text
    liftOver pennant icons for fr2 to fr3 and mm9 to mm10
• src/hg/htdocs/images/9.jpg
  • lines changed 0, context: html, text, full: html, text
    liftOver pennant icons for fr2 to fr3 and mm9 to mm10
• src/hg/lib/kgXrefPrevious.as
  • lines changed 12, context: html, text, full: html, text
    only need the .as file, not the .sql file
• src/hg/lib/kgXrefPrevious.sql
  • lines changed 22, context: html, text, full: html, text
    only need the .as file, not the .sql file
• src/hg/makeDb/doc/ce10.txt
  • lines changed 17, context: html, text, full: html, text
    liftover construction ce10 to ce6
• src/hg/makeDb/doc/fr2.txt
  • lines changed 21, context: html, text, full: html, text
    construct liftOver from fr2 to fr3
• src/hg/makeDb/doc/fr3.txt
  • lines changed 151, context: html, text, full: html, text
    initial alignment done for 8-way multiz
  • lines changed 106, context: html, text, full: html, text
    gap annotated 8-way
  • lines changed 103, context: html, text, full: html, text
    frames annotation done on 8-way
  • lines changed 142, context: html, text, full: html, text
    phylo tree distance estimate constructed from all_est
  • lines changed 34, context: html, text, full: html, text
    rework the 4d analysis to use ensGenes lifted from fr2, much better branch lengths
  • lines changed 439, context: html, text, full: html, text
    phastCons and phyloP done
  • lines changed 81, context: html, text, full: html, text
    liftOver ensGene track from fr2 to fr3
  • lines changed 7, context: html, text, full: html, text
    trackVersion hgFixed entries for ensGene v65
  • lines changed 145, context: html, text, full: html, text
    construct hgPal alignment files and download files for 8-way conservation
  • lines changed 25, context: html, text, full: html, text
    joinerCheck done, download files, and in the pushQ
  • lines changed 2, context: html, text, full: html, text
    adding URL links for external information on this assembly
• src/hg/makeDb/doc/mm10.txt
  • lines changed 77, context: html, text, full: html, text
    add lifted ensGene track from mm9
  • lines changed 7, context: html, text, full: html, text
    trackVersion hgFixed entries for ensGene v65
• src/hg/makeDb/schema/all.joiner
  • lines changed 5, context: html, text, full: html, text
    adding fr3 rules and gadMor1, latCha1 and oreNil1 chains
• src/hg/makeDb/trackDb/fugu/fr3/cons8way.html
  • lines changed 398, context: html, text, full: html, text
    initial source under edit from xenTro3 9-way
  • lines changed 10, context: html, text, full: html, text
    override for ensGene lifted indicator and update 8-way description
• src/hg/makeDb/trackDb/fugu/fr3/description.html
  • lines changed 45, context: html, text, full: html, text
    cleaned up the assembly description
• src/hg/makeDb/trackDb/fugu/fr3/gap.html
  • lines changed 49, context: html, text, full: html, text
    brought up to date
• src/hg/makeDb/trackDb/fugu/fr3/gold.html
  • lines changed 38, context: html, text, full: html, text
    up to date with proper information
• src/hg/makeDb/trackDb/fugu/fr3/trackDb.ra
  • lines changed 104, context: html, text, full: html, text
    adding 8-way conservation tracks
  • lines changed 4, context: html, text, full: html, text
    override for ensGene lifted indicator and update 8-way description
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    adding lifted ensGene from mm9
• src/hg/utils/automation/liftRMAlign.pl
  • lines changed 4, context: html, text, full: html, text
    avoid warning errors when maybeSuffix is not defined