Commits for braney

v293_preview2 to v293_base (2013-12-02 to 2013-12-09) v293

• remove erroneous subtraction of 1 from end coordinate. Fixs problemwith maf blocks of size 1 not being annotated.
  
  • src/hg/genePredToMafFrames/orgGenes.c - lines changed 1, context: html, text, full: html, text
• update GO database
  • src/hg/makeDb/doc/go.txt - lines changed 10, context: html, text, full: html, text
• make changes to the login procedures because decipher changed them.
  • src/hg/utils/otto/decipher/checkDecipher.sh - lines changed 62, context: html, text, full: html, text
  • src/hg/utils/otto/decipher/login.perl - lines changed 14, context: html, text, full: html, text
  • src/hg/utils/otto/decipher/validateDecipher.sh - lines changed 8, context: html, text, full: html, text
• don't crash if given file names with ':' in them. Fixes #12267
  • src/hg/lib/trackHub.c - lines changed 4, context: html, text, full: html, text
• add a test for repsAsMatch pslCDnaFilter flag
  • src/hg/pslCDnaFilter/tests/expected/repsAsMatchTest/filt.out - lines changed 5, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/repsAsMatchTest/keep.psl - lines changed 11, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/makefile - lines changed 4, context: html, text, full: html, text
• don't create lock files when using initialLoad to load a database. Thedatabase will still me locked. #10357
  
  • src/hg/makeDb/genbank/src/dbload/gbDbLoadStep - lines changed 8, context: html, text, full: html, text