baertsch: changes by commit

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

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