Commits for hiram

v261_base to v262_preview (2012-01-03 to 2012-01-10) v262

• adding Atlantic Cod gadMor1
  • src/hg/utils/phyloTrees/58way.nh - lines changed 24, context: html, text, full: html, text
• done through initial genome build
  • src/hg/makeDb/doc/gadMor1.txt - lines changed 121, context: html, text, full: html, text
• done with the sequence download
  • src/hg/makeDb/doc/galGal4.txt - lines changed 20, context: html, text, full: html, text
• done through initial genome build
  • src/hg/makeDb/doc/rheMac3.txt - lines changed 177, context: html, text, full: html, text
• eliminate duplicate print out of html description page for bedDetail custom tracks
  • src/hg/hgc/hgc.c - lines changed 2, context: html, text, full: html, text
• the split command needs to be 3 digit numeric expansion to avoid .gz file name
  • src/hg/utils/automation/doSimpleRepeat.pl - lines changed 1, context: html, text, full: html, text
• initial contents from makeGenomeDb.pl
  • src/hg/makeDb/trackDb/chicken/galGal4/description.html - lines changed 129, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal4/gap.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal4/gold.html - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal4/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding galGal4 to the build
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• running repeatMasker, simpleRepeats and windowMasker
  • src/hg/makeDb/doc/galGal4.txt - lines changed 445, context: html, text, full: html, text
• done with masking
  • src/hg/makeDb/doc/gadMor1.txt - lines changed 240, context: html, text, full: html, text
• masking done
  • src/hg/makeDb/doc/rheMac3.txt - lines changed 193, context: html, text, full: html, text
• last featureBits run for the gap measurements
  • src/hg/makeDb/doc/gadMor1.txt - lines changed 2, context: html, text, full: html, text
• completed masking
  • src/hg/makeDb/doc/galGal4.txt - lines changed 47, context: html, text, full: html, text
• correct done dates
  • src/hg/makeDb/doc/rheMac3.txt - lines changed 3, context: html, text, full: html, text
• improve the error messages
  • src/hg/makeDb/hgLoadBed/hgLoadBed.c - lines changed 2, context: html, text, full: html, text
• initial contents, running masking steps
  • src/hg/makeDb/doc/canFam3.txt - lines changed 375, context: html, text, full: html, text
• fixup error in file name information display
  • src/hg/makeDb/hgLoadBed/hgLoadBed.c - lines changed 1, context: html, text, full: html, text
• masking completed
  • src/hg/makeDb/doc/canFam3.txt - lines changed 85, context: html, text, full: html, text
• initial source from makeGenomeDb.pl
  • src/hg/makeDb/trackDb/chimp/panTro4/description.html - lines changed 129, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro4/gap.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro4/gold.html - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro4/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding panTro4 to the build
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• initial browser build and starting masking procedures
  • src/hg/makeDb/doc/panTro4.txt - lines changed 474, context: html, text, full: html, text
  • src/hg/makeDb/doc/saiBol1.txt - lines changed 341, context: html, text, full: html, text
• setting upstreamGeneTbl for many older genomes
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 27, context: html, text, full: html, text
• done with masking
  • src/hg/makeDb/doc/panTro4.txt - lines changed 85, context: html, text, full: html, text
  • src/hg/makeDb/doc/saiBol1.txt - lines changed 132, context: html, text, full: html, text