Commits for markd

v332_preview to v332_preview2 (2016-04-18 to 2016-05-25) v332

a6208b51039416d5be37b79b89d405aeea93be30 Mon Apr 18 13:03:32 2016 -0700

• Deal with case were CDS specifications that were create by other
  software that didn't correctly set the completeness flags create frames
  incorrectly on end-truncated sequences. This code can't possible do the
  right thing all the time if completeness isn't correctly flag, however
  this makes it more likely to do the right thing when software start from
  the beginning of the first coding defining CDS without actually setting
  completeness flags.
  
  • src/hg/genePredToGtf/genePredToGtf.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/genePred.c - lines changed 5, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/README - lines changed 4, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/expected/allCds.gp - lines changed 21, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/expected/base.gp - lines changed 1, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/expected/frame.gp - lines changed 1, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/expected/noCds.gp - lines changed 1, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/input/base.cds - lines changed 1, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/input/base.psl - lines changed 1, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/makefile - lines changed 1, context: html, text, full: html, text

fdef579bae3c23fe4057b74062858bcd60a79209 Mon Apr 18 14:42:07 2016 -0700

• removed accidently checked in garbage
  
  • src/hg/genePredToGtf/genePredToGtf.c - lines changed 1, context: html, text, full: html, text

4e0e5a68eca6f220fc5553949ccfa8b8742bce7c Mon Apr 18 16:05:27 2016 -0700

• added note in about case that is not correctly handle
  
  • src/hg/genePredToFakePsl/genePredToFakePsl.c - lines changed 6, context: html, text, full: html, text

747563375ea7f3caaaeb7a6d0092706078b0bde9 Mon Apr 18 16:57:33 2016 -0700

• simplified the code a bit
  
  • src/hg/mrnaToGene/mrnaToGene.c - lines changed 45, context: html, text, full: html, text

48254c04280712ad02cb3184108955fa3736d5fd Tue Apr 19 12:09:19 2016 -0700

• fixed incorrect label in mouse GENCODE
  
  • src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM9.ra - lines changed 1, context: html, text, full: html, text

785136193faa141057fdbe9bf48b372c69139e2a Wed Apr 20 11:59:46 2016 -0700

• added joiner rules for gencode VM9
  
  • src/hg/makeDb/schema/all.joiner - lines changed 85, context: html, text, full: html, text

3f9ec7598d1179c1802de375f06d01005306b787 Tue Apr 19 20:26:43 2016 -0700

• add program to convert transMap PSL to genePred. This handles cds for mappings that start out as genomic annotations (as opposed to alignments)
  
  • src/hg/utils/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/makefile - lines changed 6, 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/input/musstrain.mapped.psl - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/input/musstrain.src.gp - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/transMapPslToGenePred.c - lines changed 357, context: html, text, full: html, text

ff922be1fc09d6c561a9c1218e6e75cc96b6162a Wed Apr 20 18:36:55 2016 -0700

• fixed issues with reverse strand and frame
  
  • src/hg/utils/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/expected/musTest.mapped.gp - lines changed 29, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/input/musstrain.mapped.psl - lines changed 38, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/input/musstrain.src.gp - lines changed 33, 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 257, context: html, text, full: html, text

422619a0907fb407249f54733d875e585bc37c99 Wed Apr 20 20:45:30 2016 -0700

• added gap filling options
  
  • src/hg/utils/transMapPslToGenePred/tests/expected/codingFillTest.mapped.gp - lines changed 33, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/expected/fillTest.mapped.gp - lines changed 33, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/expected/nonCodingFillTest.mapped.gp - lines changed 33, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/transMapPslToGenePred.c - lines changed 31, context: html, text, full: html, text

a0a46d43875f54c997ab00b50cdf61e6e9bcc289 Thu Apr 21 11:52:08 2016 -0700

• fixed bug with negative strand gene with CDS truncation
  
  • 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/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 3, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/input/musstrain.src.gp - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/transMapPslToGenePred.c - lines changed 1, context: html, text, full: html, text

a7f4d921b739cf892c225997a3d85cea3db25f18 Thu Apr 21 16:20:24 2016 -0700

• fixed bug were polyA table wasn't being loaded
  
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 3, context: html, text, full: html, text

04d54c90e446a857d692c54652e70f050a6b486b Thu Apr 21 22:52:52 2016 -0700

• fixed bug with frame with merging block on negative strand
  
  • src/hg/utils/transMapPslToGenePred/tests/expected/codingFillTest.mapped.gp - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/expected/fillTest.mapped.gp - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/expected/musTest.mapped.gp - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/expected/nonCodingFillTest.mapped.gp - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/tests/input/musstrain.mapped.psl - lines changed 3, 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/transMapPslToGenePred.c - lines changed 6, context: html, text, full: html, text