Commits for markd

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

• 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/lib/genePred.c - lines changed 25, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/expected/allCds.gp - lines changed 7, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/expected/base.gp - lines changed 7, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/expected/cds3GapMerge.gp - lines changed 5, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/expected/frame.gp - lines changed 7, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/expected/gapMerge.gp - lines changed 4, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/expected/noCds.gp - lines changed 7, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/expected/noGapMerge.gp - lines changed 1, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/expected/trans.gp - lines changed 1, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/input/gaps.cds - lines changed 1, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/input/gaps.psl - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/gff3ToPsl.c - lines changed 22, context: html, text, full: html, text
• convert asserts to errAborts to help debug bogus GFF3 alignments (no redmine)
  
  • src/lib/psl.c - lines changed 5, context: html, text, full: html, text
• fixed problem with previous change to deal with query inserts #15803
  
  • src/hg/lib/genePred.c - lines changed 7, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/expected/allCds.gp - lines changed 7, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/expected/base.gp - lines changed 7, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/expected/cds3GapMerge.gp - lines changed 3, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/expected/frame.gp - lines changed 7, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/expected/gapMerge.gp - lines changed 3, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/expected/noCds.gp - lines changed 7, 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/gff3ToPsl.c - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/expected/grch38ToGrch37Test.psl - lines changed 20, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/input/GRCh37.p13.sizes - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/input/GRCh38.p2-GRCh37.p13.gff - lines changed 25, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/input/GRCh38.p2.sizes - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/makefile - lines changed 6, context: html, text, full: html, text
  • src/lib/psl.c - lines changed 15, context: html, text, full: html, text
• fixed invalid check for empty string detected by newer gcc (no redmine)
  
  • src/hg/utils/gff3ToPsl/gff3ToPsl.c - lines changed 1, context: html, text, full: html, text