baertsch: changes by file

review to branch (2009-11-17 to 2009-12-01) v220

• src/hg/pslCDnaGenomeMatch/makefile
  • 1.12 lines changed: 20, context: html, text, full: html, text
    add -notAlignPenalty to reduce score for non-aligning bases. Fix strand bug with -passthru
• src/hg/pslCDnaGenomeMatch/pslCDnaGenomeMatch.c
  • 1.28 lines changed: 72, context: html, text, full: html, text
    remove commented code
  • 1.27 lines changed: 132, context: html, text, full: html, text
    add -notAlignPenalty to reduce score for non-aligning bases. Fix strand bug with -passthru
• src/hg/pslCDnaGenomeMatch/expected/mrna1.psl
  • 1.2 lines changed: 6, context: html, text, full: html, text
    updated test cases to fix strand[1] and new criteria
• src/hg/pslCDnaGenomeMatch/expected/mrna12a.psl
  • 1.2 lines changed: 2, context: html, text, full: html, text
    updated test cases to fix strand[1] and new criteria
• src/hg/pslCDnaGenomeMatch/expected/mrna13b.psl
  • 1.2 lines changed: 2, context: html, text, full: html, text
    updated test cases to fix strand[1] and new criteria
• src/hg/pslCDnaGenomeMatch/expected/mrna13c.psl
  • 1.2 lines changed: 1, context: html, text, full: html, text
    updated test cases to fix strand[1] and new criteria
• src/hg/pslCDnaGenomeMatch/expected/mrna5.psl
  • 1.2 lines changed: 1, context: html, text, full: html, text
    updated test cases to fix strand[1] and new criteria
• src/hg/pslCDnaGenomeMatch/expected/mrnaDrop.psl
  • 1.2 lines changed: 399, context: html, text, full: html, text
    updated test cases to fix strand[1] and new criteria
• src/hg/pslCDnaGenomeMatch/expected/pass1733.psl
  • 1.2 lines changed: 2, context: html, text, full: html, text
    updated test cases to fix strand[1] and new criteria
• src/hg/pslCDnaGenomeMatch/expected/test15.psl
  • 1.2 lines changed: 1, context: html, text, full: html, text
    updated test cases to fix strand[1] and new criteria
• src/hg/pslCDnaGenomeMatch/expected/testBQ.psl
  • 1.2 lines changed: 6, context: html, text, full: html, text
    updated test cases to fix strand[1] and new criteria
• src/hg/pslCDnaGenomeMatch/expected/testDA9.psl
  • 1.2 lines changed: 2, context: html, text, full: html, text
    updated test cases to fix strand[1] and new criteria
• src/hg/pslCDnaGenomeMatch/input/mrnaDrop.psl
  • 1.2 lines changed: 2, context: html, text, full: html, text
    remove bad data