File Changes for markd

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

• src/hg/pslCDnaFilter/algo.txt
  • lines changed 20, context: html, text, full: html, text
    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/cDnaStats.c
  • lines changed 2, 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/pslCDnaFilter.c
  • lines changed 7, context: html, text, full: html, text
    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/tests/expected/decayMinCoverTest/filt.out
  • lines changed 1, 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/tests/expected/globalBestTest/filt.out
  • lines changed 2, 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/tests/expected/hapGlobalTest/filt.out
  • lines changed 1, 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/tests/expected/hapLocalTest/filt.out
  • lines changed 1, 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/tests/expected/hapLocalXenoTest/filt.out
  • lines changed 2, 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/tests/expected/localBestTest/filt.out
  • lines changed 2, 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/tests/expected/overlapTest/drop.psl
  • lines changed 5, 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/tests/expected/overlapTest/filt.out
  • lines changed 4, 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/tests/expected/overlapTest/keep.psl
  • lines changed 5, 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/tests/expected/overlapTest/weird.psl
  • lines changed 2, 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/tests/expected/uniqueMappedHapTest/filt.out
  • lines changed 1, 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/tests/expected/uniqueMappedTest/filt.out
  • lines changed 1, 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/tests/expected/weirdOverlapMultAlnMinCoverTest/drop.psl
  • lines changed 7, context: html, text, full: html, text
    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/tests/expected/weirdOverlapMultAlnMinCoverTest/filt.out
  • lines changed 5, context: html, text, full: html, text
    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/tests/expected/weirdOverlapMultAlnMinCoverTest/keep.psl
  • lines changed 1, context: html, text, full: html, text
    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/tests/expected/weirdOverlapMultAlnMinCoverTest/weird.psl
  • lines changed 0, context: html, text, full: html, text
    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/tests/expected/weirdOverlapMultAlnTest/drop.psl
  • lines changed 7, context: html, text, full: html, text
    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/tests/expected/weirdOverlapMultAlnTest/filt.out
  • lines changed 4, context: html, text, full: html, text
    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/tests/expected/weirdOverlapMultAlnTest/keep.psl
  • lines changed 1, context: html, text, full: html, text
    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/tests/expected/weirdOverlapMultAlnTest/weird.psl
  • lines changed 0, context: html, text, full: html, text
    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/tests/input/weirdOverlapMultAln.psl
  • lines changed 8, context: html, text, full: html, text
    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/tests/makefile
  • lines changed 16, context: html, text, full: html, text
    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.