hiram: changes by file

branch to review (2009-08-04 to 2009-08-10) v212

• src/hg/hgc/hgc.c
  • 1.1565 lines changed: 10, context: html, text, full: html, text
    Avoid Ensembl protein out link when non-coding gene
• src/hg/makeDb/doc/makeEnsembl.txt
  • 1.13 lines changed: 39, context: html, text, full: html, text
    Update hg18 to v54, and reset hgFixed entries to work properly for v55
• src/hg/makeDb/doc/tetNig2.txt
  • 1.3 lines changed: 21, context: html, text, full: html, text
    Set blat server and default position
  • 1.2 lines changed: 150, context: html, text, full: html, text
    Through masking and Ensembl v55 genes loaded
  • 1.1 lines changed: 42, context: html, text, full: html, text
    Download sequence tetNig2 browser build
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.346 lines changed: 15, context: html, text, full: html, text
    Added tetNig2
• src/hg/makeDb/schema/all.joiner
  • 1.729 lines changed: 9, context: html, text, full: html, text
    Adding loxAfr3
• src/hg/makeDb/trackDb/makefile
  • 1.274 lines changed: 1, context: html, text, full: html, text
    Adding tetNig2 to the browser build
• src/hg/makeDb/trackDb/orangutan/ponAbe2/description.html
  • 1.5 lines changed: 3, context: html, text, full: html, text
    WUSTL links have changed
• src/hg/makeDb/trackDb/sloth/choHof1/description.html
  • 1.3 lines changed: 2, context: html, text, full: html, text
    WUSTL has changed their URL locations for assemblies
• src/hg/utils/automation/EnsGeneAutomate.pm
  • 1.19 lines changed: 21, context: html, text, full: html, text
    Add version 54 for hg18 to get it to its last version
• src/hg/utils/automation/makeGenomeDb.pl
  • 1.24 lines changed: 16, context: html, text, full: html, text
    Trim down the gold and gap initial trackDb.ra entries
  • 1.23 lines changed: 6, context: html, text, full: html, text
    Adding chrM entry to the AGP file
• src/hg/utils/automation/n50.pl
  • 1.2 lines changed: 1, context: html, text, full: html, text
    improved comment, minor change
  • 1.1 lines changed: 75, context: html, text, full: html, text
    Calculate N50 values from two column sizes files
• src/hg/utils/gapToLift/gapToLift.c
  • 1.8 lines changed: 18, context: html, text, full: html, text
    Properly output lift and bed lines for chroms that have no gaps