Commits for braney

v312_preview2 to v312_base (2015-02-09 to 2015-02-16) v312

• fix checkTableCoords to actually set the exit code if it finds errors
  
  • src/hg/checkTableCoords/checkTableCoords.c - lines changed 1, context: html, text, full: html, text
• add the instructions to build a lift file to convert dbVar hg38 chrom
  names to our chrom names
  
  • src/hg/makeDb/doc/hg38/hg38.txt - lines changed 9, context: html, text, full: html, text
• don't output error message on error that is supposed to occur
  
  • src/hg/checkTableCoords/tests/makefile - lines changed 1, context: html, text, full: html, text
• some modifications to support the GENCODE as UCSC genes switch
  
  • src/hg/inc/spDb.h - lines changed 8, context: html, text, full: html, text
  • src/hg/lib/spDb.c - lines changed 16, context: html, text, full: html, text
  • src/hg/txGene/txGeneAlias/txGeneAlias.c - lines changed 2, context: html, text, full: html, text
• introductory work on program to create knownGene tables from gencode
  tables
  
  • src/hg/utils/gencodeToKnownGene/gencodeToKnownGene.c - lines changed 403, context: html, text, full: html, text
  • src/hg/utils/gencodeToKnownGene/makefile - lines changed 3, context: html, text, full: html, text
• more futzing around building UCSC genes from Gencode
  
  • src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes16.csh - lines changed 945, context: html, text, full: html, text
• update the ISCA link-out to point to the right place
  
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 1, context: html, text, full: html, text