File Changes for cline

v262_base to v263_preview (2012-01-24 to 2012-01-31) v263

• src/hg/lib/kgXref.sql
  • lines changed 9, context: html, text, full: html, text
    Addressing code review feedback - thanks, Braney! Restored some lost indices, and expanded two description lines slightly
• src/hg/lib/knownCanonical.as
  • lines changed 2, context: html, text, full: html, text
    Addressing code review feedback - thanks, Braney! Restored some lost indices, and expanded two description lines slightly
  • lines changed 1, context: html, text, full: html, text
    Made the description of the protein field more generic, reflecting that the protein accession might or might not be the UniProt ID
  • lines changed 1, context: html, text, full: html, text
    Changing a description line - for the last time. I refuse to change it again\!
• src/hg/lib/knownCanonical.sql
  • lines changed 5, context: html, text, full: html, text
    Follow-up to changing knownCanonical.as as part of this week's code review: changing the products of knownCanonical.as
  • lines changed 1, context: html, text, full: html, text
    Made the description of the protein field more generic, reflecting that the protein accession might or might not be the UniProt ID
  • lines changed 1, context: html, text, full: html, text
    Changing a description line - for the last time. I refuse to change it again\!
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 16, context: html, text, full: html, text
    1: when I tried to load the blast tabs at the end of the script, I discovered that some of the files I needed had been deleted earlier on. So, I moved that cleanup step to the very end, after the loading of the blast tabs. 2: in building the keggPathway table, replaced a SELECT statement with a SELECT DISTINCT, to avoid (more) tables of millions of duplicated lines
  • lines changed 2, context: html, text, full: html, text
    addressing note 12 in Redmine 5674: set up the code so that in future executions, whenever a new known Gene blat server is set up, the server is identified by version number along with the keyword hg19Kg
  • lines changed 2, context: html, text, full: html, text
    addressing note 12 in Redmine 5674: set up the code so that in future executions, whenever a new known Gene blat server is set up, the server is identified by version number along with the keyword hg19Kg
• src/hg/makeDb/trackDb/human/hg19/knownGeneNew.html
  • lines changed 1, context: html, text, full: html, text
    A few last-minute documentation things for UCSC Genes
  • lines changed 2, context: html, text, full: html, text
    Fixing a grammatical error
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    A few last-minute documentation things for UCSC Genes
• src/hg/txGene/txGeneXref/txGeneXref.c
  • lines changed 13, context: html, text, full: html, text
    Changes to address git #2 note # 91 (see also # 6752). The descriptions were sometimes inconsistent with the gene symbol. This arose when the refLink description field was blank, and the code would end up pulling descriptions from GenBank records. And of course, every so often there's some paralog in GenBank that just aligns in the wrong place... So here's the new plan. For transcripts that overlap a RefSeq (i.e. refseq is not ""), get the gene symbol from refLink and the description from description. If the description is still blank when it comes time to look at the GenBank records, don\'t even bother with the GenBank records if the transcript is related to a RefSeq, just leave the descriptions blank (this shoudl be fairly rare).