Commits for hiram

v260_preview to v260_preview2 (2011-11-15 to 2011-11-22) v260

• eliminate felCat3 from identifier ensemblTranscriptId checks
  • src/hg/makeDb/schema/all.joiner - lines changed 5, context: html, text, full: html, text
• no refseq natives for gorGor3
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 1, context: html, text, full: html, text
• adding proper search rule for gold table
  • src/hg/makeDb/trackDb/gorilla/gorGor3/trackDb.ra - lines changed 7, context: html, text, full: html, text
• clarify language issues and formatting
  • src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html - lines changed 8, context: html, text, full: html, text
• remove all_mrna and all_est and fixup gold search
  • src/hg/makeDb/trackDb/gibbon/nomLeu1/trackDb.ra - lines changed 32, context: html, text, full: html, text
• allow refLink searches to work when accessions have version numbers (ignore the accession version number) RedMine issue 6040
  • src/hg/lib/hgFind.c - lines changed 12, context: html, text, full: html, text
• add a two item name between region display example
  • src/hg/makeDb/trackDb/gorilla/gorGor3/description.html - lines changed 4, context: html, text, full: html, text
• indicate NM version number searches ignore the version extension
  • src/hg/makeDb/trackDb/gorilla/gorGor3/description.html - lines changed 4, context: html, text, full: html, text
• load a sorted fa.out file to satisify the QA ordered table check
  • src/hg/utils/automation/doRepeatMasker.pl - lines changed 16, context: html, text, full: html, text
• eliminate teh obsolete all_mrna and all_est entries in the initial trackDb.ra file
  • src/hg/utils/automation/makeGenomeDb.pl - lines changed 37, context: html, text, full: html, text
• initial files from makeGenomeDb.pl
  • src/hg/makeDb/trackDb/fugu/fr3/description.html - lines changed 129, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/fr3/gap.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/fr3/gold.html - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/fr3/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding fr3 fugu to the build
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• initial genome build with repeat masker, simple repeats, and gaps fixed up
  • src/hg/makeDb/doc/fr3.txt - lines changed 236, context: html, text, full: html, text
• one line too much in the head to sorted operation
  • src/hg/utils/automation/doRepeatMasker.pl - lines changed 1, context: html, text, full: html, text
• adding chainNet overrides and proper search for gold track
  • src/hg/makeDb/trackDb/gorilla/gorGor3/trackDb.chainNet.ra - lines changed 40, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gorilla/gorGor3/trackDb.ra - lines changed 7, context: html, text, full: html, text
• set priorities for gorGor3 chain net tracks
  • src/hg/makeDb/trackDb/orangutan/trackDb.chainNet.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/trackDb.chainNet.ra - lines changed 4, context: html, text, full: html, text
• overrides for hg19 and gorGor3
  • src/hg/makeDb/trackDb/gibbon/trackDb.chainNet.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gibbon/trackDb.ra - lines changed 3, context: html, text, full: html, text
• fixup URL for alternate sequence
  • src/hg/makeDb/trackDb/human/hg19/altSeqComposite5.ra - lines changed 2, context: html, text, full: html, text
• windowMasker and blat server now running
  • src/hg/makeDb/doc/fr3.txt - lines changed 123, context: html, text, full: html, text
• adding definitions for fr3 Fugu
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 16, context: html, text, full: html, text
• proper searching for gold table
  • src/hg/makeDb/trackDb/fugu/fr3/trackDb.ra - lines changed 6, context: html, text, full: html, text
• phylo tree for Gorilla 11-way primate alignment
  • src/hg/htdocs/images/phylo/gorGor3_11way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• catch up some ancient instructions for Baboon
  • src/hg/makeDb/doc/papHam1.txt - lines changed 193, context: html, text, full: html, text
• add link to WGS Traces information for these assemblies
  • src/hg/makeDb/doc/anoCar2.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/calJac3.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/danRer7.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/melGal1.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/micMur1.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/otoGar1.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/panTro3.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/papHam1.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/ponAbe2.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/rheMac2.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/tarSyr1.txt - lines changed 3, context: html, text, full: html, text
• running synNet maf split for 11-way alignment
  • src/hg/makeDb/doc/gorGor3.txt - lines changed 31, context: html, text, full: html, text