Commits for angie

v376_base to v377_preview (2019-01-14 to 2019-01-21) v377

15583bcb1652d3ca3dab7d1a96c21e2c3c133613 Tue Jan 15 09:53:14 2019 -0800

• Adding makeDb/doc files for hg19 and hg38 patch updates. refs #18853
  • src/hg/makeDb/doc/grcH37P13.txt - lines changed 300, context: html, text, full: html, text
  • src/hg/makeDb/doc/grcHhh38/grcH38P11.txt - lines changed 475, context: html, text, full: html, text
  • src/hg/makeDb/doc/grcHhh38/grcH38P12.txt - lines changed 385, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.patchUpdate.13.txt - lines changed 715, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.scanAssemblyReport.pl - lines changed 120, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/grcH38P11.txt - lines changed 475, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/grcH38P12.txt - lines changed 385, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/patchUpdate.11.txt - lines changed 578, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/patchUpdate.12.txt - lines changed 634, context: html, text, full: html, text

355d302871339c7103597454b674aba7fc9e4f4c Tue Jan 15 12:29:35 2019 -0800

• Oops, liftOver -genePred support for -multiple was not implemented -- but there was no error message about that. Add error message for now, then add -multiple support later. refs #18855
  • src/hg/liftOver/liftOver.c - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.patchUpdate.13.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/patchUpdate.11.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/patchUpdate.12.txt - lines changed 1, context: html, text, full: html, text

5b83a4f3758e71c48c76f3235f7a1924c21b4ae2 Tue Jan 15 13:21:18 2019 -0800

• Implement liftOver -multiple -genePred; update gtexGeneModel with all the alts/patches. refs #18855
  • src/hg/inc/liftOver.h - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/liftOver.c - lines changed 22, context: html, text, full: html, text
  • src/hg/liftOver/liftOver.c - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.patchUpdate.13.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/patchUpdate.11.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/patchUpdate.12.txt - lines changed 3, context: html, text, full: html, text

c49908e3df61eaad9dc356a0e8e17e4547a323a9 Wed Jan 16 15:03:56 2019 -0800

• After processing an uploaded file of user regions, remove its contents from the cart. Users have uploaded some very large files as identifier lists.
  • src/hg/hgTables/userRegions.c - lines changed 1, context: html, text, full: html, text