File Changes for cline

v262_preview2 to v262_base (2012-01-17 to 2012-01-24) v262

• src/hg/hgGene/info.c
  • lines changed 8, context: html, text, full: html, text
    Changing the wording around RNA accession, addressing Redmine #5983
• src/hg/inc/hgnc.h
  • lines changed 101, context: html, text, full: html, text
    Updated the HGNC object so that it contains all the fields from the HGNC standard download tables
• src/hg/inc/kgXref.h
  • lines changed 2, context: html, text, full: html, text
    In response to Redmine #6660, which rightly points out that the table descriptors are outdated where they reference SwissProt protein IDs, updated the table descriptors to indicate that those fields are actually UniProt IDs
• src/hg/lib/hgnc.as
  • lines changed 25, context: html, text, full: html, text
    Updated the HGNC object so that it contains all the fields from the HGNC standard download tables
• src/hg/lib/hgnc.c
  • lines changed 435, context: html, text, full: html, text
    Updated the HGNC object so that it contains all the fields from the HGNC standard download tables
• src/hg/lib/hgnc.sql
  • lines changed 41, context: html, text, full: html, text
    Updated the HGNC object so that it contains all the fields from the HGNC standard download tables
• src/hg/lib/kgXref.as
  • lines changed 2, context: html, text, full: html, text
    In response to Redmine #6660, which rightly points out that the table descriptors are outdated where they reference SwissProt protein IDs, updated the table descriptors to indicate that those fields are actually UniProt IDs
• src/hg/lib/kgXref.sql
  • lines changed 11, context: html, text, full: html, text
    In response to Redmine #6660, which rightly points out that the table descriptors are outdated where they reference SwissProt protein IDs, updated the table descriptors to indicate that those fields are actually UniProt IDs
• src/hg/lib/knownCanonical.as
  • lines changed 2, context: html, text, full: html, text
    Addressing Redmine bug # 6661 by changing the wording for the chromStart and chromEnd fields to indicate that they correspond to txStart and txEnd respectively for + strand genes, not for all genes
  • lines changed 1, context: html, text, full: html, text
    In response to Redmine #6660, which rightly points out that the table descriptors are outdated where they reference SwissProt protein IDs, updated the table descriptors to indicate that those fields are actually UniProt IDs
• src/hg/lib/knownCanonical.c
  • lines changed 146, context: html, text, full: html, text
    Addressing Redmine bug # 6661 by changing the wording for the chromStart and chromEnd fields to indicate that they correspond to txStart and txEnd respectively for + strand genes, not for all genes
• src/hg/lib/knownCanonical.sql
  • lines changed 6, context: html, text, full: html, text
    Addressing Redmine bug # 6661 by changing the wording for the chromStart and chromEnd fields to indicate that they correspond to txStart and txEnd respectively for + strand genes, not for all genes
  • lines changed 1, context: html, text, full: html, text
    In response to Redmine #6660, which rightly points out that the table descriptors are outdated where they reference SwissProt protein IDs, updated the table descriptors to indicate that those fields are actually UniProt IDs
• src/hg/makeDb/doc/hg19.txt
  • lines changed 13, context: html, text, full: html, text
    Added commands to download the HGNC data and load it into the hg19 database
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 1, context: html, text, full: html, text
    a joiner check error revealed that the bioCyc tables had been built with the wrong version of the knownGenes table. They'd been built against the version on hgwdev rather than the version being built in the tempDb. Fixed that.
  • lines changed 33, context: html, text, full: html, text
    In response to Redmine #5180, in all cases where a knownTo* table was not built by hgMapToGene (as most are), added a mysql delete statement to remove antibody parts from the knownTo* table after the table gets loaded
• src/hg/txGene/txGeneXref/txGeneXref.c
  • lines changed 5, context: html, text, full: html, text
    Cleaning up the code in response to some excellent code review feedback from Angie