Commits for markd

v332_preview2 to v332_base (2016-04-25 to 2016-05-02) v332

f3406d68a298ea5b567b5d67bc05db6ecabc3b92 Tue Apr 26 12:29:03 2016 -0700

• fixed bug with merger negative strand gaps due to incorrect frame test
  
  • src/hg/utils/transMapPslToGenePred/tests/expected/codingFillTest.mapped.gp - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/expected/fillTest.mapped.gp - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/expected/musTest.mapped.gp - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/expected/nonCodingFillTest.mapped.gp - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/input/musstrain.mapped.psl - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/input/musstrain.src.gp - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/transMapPslToGenePred.c - lines changed 13, context: html, text, full: html, text

48c9b138b777d310591c9a4e0b3efdd768b9679d Tue Apr 26 19:11:47 2016 -0700

• fixed a bug with frame when gap filling on reverse strand
  
  • src/hg/utils/transMapPslToGenePred/tests/expected/codingFillTest.mapped.gp - lines changed 10, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/expected/fillTest.mapped.gp - lines changed 10, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/expected/fillTest30.mapped.gp - lines changed 37, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/expected/musTest.mapped.gp - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/expected/nonCodingFillTest.mapped.gp - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/input/musstrain.mapped.psl - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/input/musstrain.src.gp - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/makefile - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/transMapPslToGenePred.c - lines changed 13, context: html, text, full: html, text

5a54acb02ba08533f895379e2bfd42d0ef779c8e Fri Apr 29 09:45:33 2016 -0700

• improved documentation on CDS issues
  
  • src/hg/lib/genePred.c - lines changed 9, context: html, text, full: html, text

885abd78d6f56c4dbca20603d976491d3cfceddf Fri Apr 29 09:56:32 2016 -0700

• added new test cases
  
  • src/hg/utils/transMapPslToGenePred/tests/expected/codingFillTest.mapped.gp - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/expected/fillTest.mapped.gp - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/expected/fillTest30.mapped.gp - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/expected/musTest.mapped.gp - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/expected/nonCodingFillTest.mapped.gp - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/input/musstrain.mapped.psl - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/input/musstrain.src.gp - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/transMapPslToGenePred.c - lines changed 3, context: html, text, full: html, text

6c2a52a6839a66ea22dc531d5ce3e3a8c3619b4e Fri Apr 29 12:52:20 2016 -0700

• V24lift37 doesn't have exon supports table, remove it from trackDb
  
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV24lift37.ra - lines changed 1, context: html, text, full: html, text