markd: changes by commit

branch to review (2010-03-23 to 2010-03-30) v228

• make functionality match usage message by making the database optional on the command line
  • src/hg/hgsql/hgsql.c 1.11 - lines changed: 1, context: html, text, full: html, text
• fixed stupid bug that caused -idMatch to do the exact opposite of what it was suppose to do
  • src/hg/overlapSelect/selectTable.c 1.32 - lines changed: 2, context: html, text, full: html, text
  • src/hg/overlapSelect/tests/expected/idMatchSimple.gp 1.1 - lines changed: 1, context: html, text, full: html, text
  • src/hg/overlapSelect/tests/expected/idMatchSimpleNon.gp 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/overlapSelect/tests/expected/psl_idMatch.drop.psl 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/overlapSelect/tests/expected/psl_idMatch.psl 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/overlapSelect/tests/expected/psl_idMatch_non.drop.psl 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/overlapSelect/tests/expected/psl_idMatch_non.psl 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/overlapSelect/tests/input/idMatchSimple1.gp 1.1 - lines changed: 1, context: html, text, full: html, text
  • src/hg/overlapSelect/tests/input/idMatchSimple2.gp 1.1 - lines changed: 1, context: html, text, full: html, text
  • src/hg/overlapSelect/tests/makefile 1.36 - lines changed: 10, context: html, text, full: html, text
• prevent permission errors when installing scripts
  • src/hg/makeDb/hgCalStat/makefile 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/utils/cvsTools/makefile 1.5 - lines changed: 2, context: html, text, full: html, text
• don't free cached connection with sqlDisconnect
  • src/hg/hgTables/bedList.c 1.70 - lines changed: 1, context: html, text, full: html, text
• readability changes suggest by Tim
  • src/lib/pipeline.c 1.24 - lines changed: 15, context: html, text, full: html, text
• clarified error handling
  • src/hg/utils/gff3ToGenePred/gff3ToGenePred.c 1.6 - lines changed: 3, context: html, text, full: html, text