hiram: changes by commit

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

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