Commits for markd

v362_base to v363_preview (2018-03-05 to 2018-03-12) v363

5899cbd4120fc82ba0939dce519582841db961f7 Thu Mar 8 11:38:07 2018 -0800

• Add support for GENCODE protein id to wgEncodeGencodeAttrs* table. For backwards compatibility with existing tables, this was added as the last column of the table and the code checks for it's presences. RM 21077
  • src/hg/hgc/gencodeClick.c - lines changed 26, context: html, text, full: html, text
  • src/hg/inc/encode/wgEncodeGencodeAttrs.h - lines changed 9, context: html, text, full: html, text
  • src/hg/lib/encode/wgEncodeGencodeAttrs.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/encode/wgEncodeGencodeAttrs.c - lines changed 22, context: html, text, full: html, text
  • src/hg/lib/encode/wgEncodeGencodeAttrs.sql - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 2, context: html, text, full: html, text

2b39fab6c6a54dde12024faaef0f32c8af0f7f16 Thu Mar 8 12:18:30 2018 -0800

• added index to wgEncodeGencodeAttrs proteinId column
  • src/hg/lib/encode/wgEncodeGencodeAttrs.sql - lines changed 2, context: html, text, full: html, text

c37711d09c8d3951e4e36144c7abfd0b6e3bff71 Thu Mar 8 19:15:01 2018 -0800

• added -refseqHacks option to handle special refseq cases. Initially this handles gene with direct CDS where transcript accession in on the CDS record RM21079
  • src/hg/utils/gff3ToGenePred/gff3ToGenePred.c - lines changed 40, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/ncbiProblemsTest.attrs - lines changed 26, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/ncbiProblemsTest.gp - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/ncbiProblemsTest.out - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/useNameTest.gp - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/input/ncbiProblems.gff3 - lines changed 16, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/makefile - lines changed 1, context: html, text, full: html, text

e09f1a98e3dca1819c5fd9c834d2c85469c3df2d Fri Mar 9 10:05:25 2018 -0800

• added proteinId to attributes for GENCODE V19, VM16, and V27 for use by VAI
  • src/hg/makeDb/doc/hg19.txt - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/hg38.txt - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/schema/all.joiner - lines changed 1, context: html, text, full: html, text