Commits for markd

v279_preview to v279_preview2 (2013-01-29 to 2013-02-05) v279

• Fixed handling of multiple indentical overlapping alignments create by mappingproteins via mRNAs, along with a couple of weird alignments. This results in
  all alignments being kept. The weird overlap was moved until later so that
  -bestOverlap and other filters still work.
  
  • src/hg/pslCDnaFilter/algo.txt - lines changed 20, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/pslCDnaFilter.c - lines changed 7, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/weirdOverlapMultAlnMinCoverTest/drop.psl - lines changed 7, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/weirdOverlapMultAlnMinCoverTest/filt.out - lines changed 5, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/weirdOverlapMultAlnMinCoverTest/keep.psl - lines changed 1, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/weirdOverlapMultAlnMinCoverTest/weird.psl - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/pslCDnaFilter/tests/expected/weirdOverlapMultAlnTest/drop.psl - lines changed 7, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/weirdOverlapMultAlnTest/filt.out - lines changed 4, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/weirdOverlapMultAlnTest/keep.psl - lines changed 1, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/weirdOverlapMultAlnTest/weird.psl - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/pslCDnaFilter/tests/input/weirdOverlapMultAln.psl - lines changed 8, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/makefile - lines changed 16, context: html, text, full: html, text
• Minor changes relative to previous weird overlap change. Print stats in the order the filters happen and fixed test output
  • src/hg/pslCDnaFilter/cDnaStats.c - lines changed 2, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/decayMinCoverTest/filt.out - lines changed 1, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/globalBestTest/filt.out - lines changed 2, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/hapGlobalTest/filt.out - lines changed 1, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/hapLocalTest/filt.out - lines changed 1, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/hapLocalXenoTest/filt.out - lines changed 2, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/localBestTest/filt.out - lines changed 2, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/overlapTest/drop.psl - lines changed 5, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/overlapTest/filt.out - lines changed 4, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/overlapTest/keep.psl - lines changed 5, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/overlapTest/weird.psl - lines changed 2, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/uniqueMappedHapTest/filt.out - lines changed 1, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/uniqueMappedTest/filt.out - lines changed 1, context: html, text, full: html, text