Commits for markd

v360_base to v361_preview (2018-01-22 to 2018-01-29) v361

03d79bf4ff976c1c0f7327d91e8b9d9adc70cefd Tue Jan 23 21:55:36 2018 -0800

• do a better job converting NCBI [CDJV]_gene_segment GFF3 annotations. This avoids split into genePreds. Another evening wasted with bioinformatics file formats
  • src/hg/utils/gff3ToGenePred/gff3ToGenePred.c - lines changed 111, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/ncbiSegmentsTest.attrs - lines changed 77, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/ncbiSegmentsTest.gp - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/input/ncbiSegments.gff3 - lines changed 35, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/makefile - lines changed 7, context: html, text, full: html, text
  • src/inc/gff3.h - lines changed 12, context: html, text, full: html, text
  • src/lib/gff3.c - lines changed 30, context: html, text, full: html, text

c38255cd365b9742bf47b39954cbd26770bef21f Thu Jan 25 17:29:09 2018 -0800

• changed handling of previous change NCBI immuno segments to just discard the gene-level CDS, as moving them to the transcript level brought out CDS/exon inconsitencies in the NCBI human and mouse files
  • src/hg/utils/gff3ToGenePred/gff3ToGenePred.c - lines changed 12, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/ncbiSegmentsTest.attrs - lines changed 194, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/ncbiSegmentsTest.gp - lines changed 14, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/ncbiSegmentsTest.out - lines changed 12, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/input/ncbiSegments.gff3 - lines changed 89, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/makefile - lines changed 2, context: html, text, full: html, text