Commits for angie

v391_base to v392_preview (2019-12-02 to 2019-12-09) v392

b5c23fe6c6f64e514ddfaceb2d9f0a08b8db15b9 Thu Dec 5 11:25:15 2019 -0800

• Updating SPDI reference from bioRxiv to publication in Bioinformatics (& PubMed). refs #23283
  • src/hg/makeDb/trackDb/human/dbSnp153Composite.html - lines changed 6, context: html, text, full: html, text

a18829b3e826a0e9c52cb145ff0db94b58e8e01d Fri Dec 6 13:09:57 2019 -0800

• bigDbSnp: fix colors in dense mode by defining itemColor in addition to itemNameColor and sorting items so that most severe consequences are drawn on top. If maxItems is exceeded, warn user. refs #23283
  • src/hg/hgTracks/variation.c - lines changed 60, context: html, text, full: html, text

88fd02db3cab8dff3040029460e821af7bf976d2 Fri Dec 6 15:29:15 2019 -0800

• Update of hg38 ncbiRefSeq changed gene symbol from YARS to YARS1 -- update hgvs test files.
  • src/hg/lib/tests/expected/hgvs/validTerms.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/tests/input/hgvs/validTerms.txt - lines changed 1, context: html, text, full: html, text

758b07c41f9b7671b80379569a42ef5bf6fb4f64 Fri Dec 6 15:59:28 2019 -0800

• Update of hg38 ncbiRefSeq changed NM_020469.2 to .3 -- update hgvsToVcf test files.
  • src/hg/utils/hgvsToVcf/tests/expected/testShifting.vcf - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/hgvsToVcf/tests/input/testShifting.txt - lines changed 5, context: html, text, full: html, text

86ca6b671c952324dacf42375e51234c9a99be52 Fri Dec 6 16:18:55 2019 -0800

• Update of hg38 ncbiRefSeq changed a bunch of NM_ versions -- update vcfToHgvs test files.
  • src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab - lines changed 13, context: html, text, full: html, text