Commits for markd

v242_base to v243_preview (2010-10-12 to 2010-10-19) v243

• added handling of misidentified psiblast files
  • src/hg/blastToPsl/blastXmlToPsl.c - lines changed 47, context: html, text, full: html, text
  • src/hg/blastToPsl/tests/expected/misclassedPsiBlastTest.bscores - lines changed 11, context: html, text, full: html, text
  • src/hg/blastToPsl/tests/expected/misclassedPsiBlastTest.psl - lines changed 10, context: html, text, full: html, text
  • src/hg/blastToPsl/tests/input/misclassed.psiBlast.xml - lines changed 483, context: html, text, full: html, text
  • src/hg/blastToPsl/tests/makefile - lines changed 10, context: html, text, full: html, text
• added options to control max number of errors reports
  • src/hg/utils/gff3ToGenePred/gff3ToGenePred.c - lines changed 19, context: html, text, full: html, text
• added RefSeq gene predictions to Rhesus at the request of NCBI
  • src/hg/makeDb/doc/rheMac2.txt - lines changed 38, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/refGenePred.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/trackDb.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
• converted rheMac2 refPreds to full RefSeq annotation track at request of NCBI
  • src/hg/makeDb/doc/rheMac2.txt - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/refSeqAnnon.html - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/trackDb.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
• spDbAddVarSplice was not being built
  • src/hg/protein/makefile - lines changed 1, context: html, text, full: html, text
• imported new uniport
  • src/hg/makeDb/doc/uniProt/sp101005.txt - lines changed 50, context: html, text, full: html, text
• redid refseq annonotation track to include all refseq mappings
  • src/hg/makeDb/doc/rheMac2.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/refGenePred.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/trackDb.ra - lines changed 11, context: html, text, full: html, text