File Changes for markd

v320_base to v321_preview (2015-08-03 to 2015-08-21) v321

• src/hg/lib/genePred.c
  • lines changed 25, context: html, text, full: html, text
    Fixed with psl to genePred frame correction working when there
    is target deletion. A lot of test cases changed as they
    were constructed from transMap and so had a lot of indels. (#15803)
    
  • lines changed 7, context: html, text, full: html, text
    fixed problem with previous change to deal with query inserts #15803
    
• src/hg/mrnaToGene/tests/expected/allCds.gp
  • lines changed 7, context: html, text, full: html, text
    Fixed with psl to genePred frame correction working when there
    is target deletion. A lot of test cases changed as they
    were constructed from transMap and so had a lot of indels. (#15803)
    
  • lines changed 7, context: html, text, full: html, text
    fixed problem with previous change to deal with query inserts #15803
    
• src/hg/mrnaToGene/tests/expected/base.gp
  • lines changed 7, context: html, text, full: html, text
    Fixed with psl to genePred frame correction working when there
    is target deletion. A lot of test cases changed as they
    were constructed from transMap and so had a lot of indels. (#15803)
    
  • lines changed 7, context: html, text, full: html, text
    fixed problem with previous change to deal with query inserts #15803
    
• src/hg/mrnaToGene/tests/expected/cds3GapMerge.gp
  • lines changed 5, context: html, text, full: html, text
    Fixed with psl to genePred frame correction working when there
    is target deletion. A lot of test cases changed as they
    were constructed from transMap and so had a lot of indels. (#15803)
    
  • lines changed 3, context: html, text, full: html, text
    fixed problem with previous change to deal with query inserts #15803
    
• src/hg/mrnaToGene/tests/expected/frame.gp
  • lines changed 7, context: html, text, full: html, text
    Fixed with psl to genePred frame correction working when there
    is target deletion. A lot of test cases changed as they
    were constructed from transMap and so had a lot of indels. (#15803)
    
  • lines changed 7, context: html, text, full: html, text
    fixed problem with previous change to deal with query inserts #15803
    
• src/hg/mrnaToGene/tests/expected/gapMerge.gp
  • lines changed 4, context: html, text, full: html, text
    Fixed with psl to genePred frame correction working when there
    is target deletion. A lot of test cases changed as they
    were constructed from transMap and so had a lot of indels. (#15803)
    
  • lines changed 3, context: html, text, full: html, text
    fixed problem with previous change to deal with query inserts #15803
    
• src/hg/mrnaToGene/tests/expected/noCds.gp
  • lines changed 7, context: html, text, full: html, text
    Fixed with psl to genePred frame correction working when there
    is target deletion. A lot of test cases changed as they
    were constructed from transMap and so had a lot of indels. (#15803)
    
  • lines changed 7, context: html, text, full: html, text
    fixed problem with previous change to deal with query inserts #15803
    
• src/hg/mrnaToGene/tests/expected/noGapMerge.gp
  • lines changed 1, context: html, text, full: html, text
    Fixed with psl to genePred frame correction working when there
    is target deletion. A lot of test cases changed as they
    were constructed from transMap and so had a lot of indels. (#15803)
    
• src/hg/mrnaToGene/tests/expected/trans.gp
  • lines changed 1, context: html, text, full: html, text
    Fixed with psl to genePred frame correction working when there
    is target deletion. A lot of test cases changed as they
    were constructed from transMap and so had a lot of indels. (#15803)
    
• src/hg/mrnaToGene/tests/input/gaps.cds
  • lines changed 1, context: html, text, full: html, text
    Fixed with psl to genePred frame correction working when there
    is target deletion. A lot of test cases changed as they
    were constructed from transMap and so had a lot of indels. (#15803)
    
• src/hg/mrnaToGene/tests/input/gaps.psl
  • lines changed 2, context: html, text, full: html, text
    Fixed with psl to genePred frame correction working when there
    is target deletion. A lot of test cases changed as they
    were constructed from transMap and so had a lot of indels. (#15803)
    
• src/hg/utils/gff3ToPsl/gff3ToPsl.c
  • lines changed 22, context: html, text, full: html, text
    Fixed with psl to genePred frame correction working when there
    is target deletion. A lot of test cases changed as they
    were constructed from transMap and so had a lot of indels. (#15803)
    
  • lines changed 5, context: html, text, full: html, text
    fixed bug converting GFF3 alignments to PSL when alignments started or ended with indels (no redmine)
    
  • lines changed 1, context: html, text, full: html, text
    fixed invalid check for empty string detected by newer gcc (no redmine)
    
• src/hg/utils/gff3ToPsl/tests/expected/grch38ToGrch37Test.psl
  • lines changed 20, context: html, text, full: html, text
    fixed bug converting GFF3 alignments to PSL when alignments started or ended with indels (no redmine)
    
• src/hg/utils/gff3ToPsl/tests/input/GRCh37.p13.sizes
  • lines changed 1, context: html, text, full: html, text
    fixed bug converting GFF3 alignments to PSL when alignments started or ended with indels (no redmine)
    
• src/hg/utils/gff3ToPsl/tests/input/GRCh38.p2-GRCh37.p13.gff
  • lines changed 25, context: html, text, full: html, text
    fixed bug converting GFF3 alignments to PSL when alignments started or ended with indels (no redmine)
    
• src/hg/utils/gff3ToPsl/tests/input/GRCh38.p2.sizes
  • lines changed 6, context: html, text, full: html, text
    fixed bug converting GFF3 alignments to PSL when alignments started or ended with indels (no redmine)
    
• src/hg/utils/gff3ToPsl/tests/makefile
  • lines changed 6, context: html, text, full: html, text
    fixed bug converting GFF3 alignments to PSL when alignments started or ended with indels (no redmine)
    
• src/lib/psl.c
  • lines changed 5, context: html, text, full: html, text
    convert asserts to errAborts to help debug bogus GFF3 alignments (no redmine)
    
  • lines changed 15, context: html, text, full: html, text
    fixed bug converting GFF3 alignments to PSL when alignments started or ended with indels (no redmine)