markd: changes by file

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

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