Commits for braney

v335_preview2 to v335_base (2016-06-27 to 2016-07-04) v335

e2bad0b45e1e163a9f4b84fb3c76e93994e9a208 Mon Jun 27 15:36:28 2016 -0700

• Old UCSC Genes description
  
  • src/hg/makeDb/trackDb/human/hg38/knownGeneOld9.html - lines changed 17, context: html, text, full: html, text

12e63280f4c2dac4dcba582d94dfdedc731f342a Mon Jun 27 15:39:13 2016 -0700

• rebuild CDS FASTA downloads for hg38 knownGene and knownCanonical
  
  • src/hg/makeDb/doc/hg38/multiz100way.txt - lines changed 15, context: html, text, full: html, text

6602ea77fd2e1cf9d0b993076805f551dd735c62 Mon Jun 27 15:44:00 2016 -0700

• formatting fix in doc
  
  • src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes17.sh - lines changed 4, context: html, text, full: html, text

fef43d40a51eb99f7abb3f289fac9218c7c7c24e Tue Jun 28 00:52:49 2016 -0700

• redo refGene CDS Fasta alignments with hg19 multiz100way
  
  • src/hg/makeDb/doc/hg19.txt - lines changed 9, context: html, text, full: html, text

d229ccd25b8ed02ab143f8cfc2e174ebd749a03b Tue Jun 28 17:37:20 2016 -0700

• deal with table names in idXref statements of the form db.table
  
  • src/hg/hgTables/identifiers.c - lines changed 6, context: html, text, full: html, text

113f2763842116b69b0bdb4d6acc05f006cc5dc9 Wed Jun 29 10:27:13 2016 -0700

• add isPcr gfServer for hg38 knownGene
  
  • src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes17.sh - lines changed 4, context: html, text, full: html, text

19dbed83451bec7177ac6ebbbd17b161e1609c32 Wed Jun 29 12:23:18 2016 -0700

• fix up hg38 otherOrgs.ra to delete links to other species without hgGene
  
  • src/hg/hgGene/hgGeneData/Human/hg15/otherOrgs.ra - lines changed 18, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Human/hg16/otherOrgs.ra - lines changed 17, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Human/hg17/otherOrgs.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Human/hg18/otherOrgs.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Human/hg19/otherOrgs.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Human/hg38/otherOrgs.ra - lines changed 7, context: html, text, full: html, text

bce4fe1b88cbe14c14ba8292ee15fa420cf908bb Wed Jun 29 12:24:19 2016 -0700

• delete Human otherOrgs.ra
  
  • src/hg/hgGene/hgGeneData/Human/otherOrgs.ra - lines changed 24, context: html, text, full: html, text

10fba1d5b5154cae1299fd79f55d9d582815a207 Wed Jun 29 15:10:35 2016 -0700

• make sure CDS field is null and error out with message on protein psl
  
  • src/hg/utils/pslToBigPsl/pslToBigPsl.c - lines changed 4, context: html, text, full: html, text

65aee15f89102180ee10261f0da584856bac6ee4 Fri Jul 1 14:18:10 2016 -0700

• add bigChain to the list of bigBed formats in trackDb.h
  
  • src/hg/inc/trackDb.h - lines changed 1, context: html, text, full: html, text