Commits for angie

v396_preview to v396_preview2 (2020-03-16 to 2020-03-23) v396

5c8f8925eb335bb375595e839368c3f7594ea7e4 Mon Mar 16 12:24:10 2020 -0700

• Libify code that counts genotypes correctly from vcfClick.c and use it in vcfTrack.c. refs #24623, fixes #25165
  • src/hg/hgTracks/vcfTrack.c - lines changed 44, context: html, text, full: html, text
  • src/hg/hgc/vcfClick.c - lines changed 58, context: html, text, full: html, text
  • src/inc/vcf.h - lines changed 15, context: html, text, full: html, text
  • src/lib/vcf.c - lines changed 68, context: html, text, full: html, text

42d91822ec103cfcc74e9f69b39d3ad8d886c278 Wed Mar 18 15:25:15 2020 -0700

• Add a new trackDb setting hapClusterMethod and corresponding UI option for drawing haplotypes in VCF file order instead of clustering. refs #25197 Applied the new setting to mm10 strainSNPs and increased its default height so that strain labels appear in the left label area.
  • src/hg/hgTracks/vcfTrack.c - lines changed 134, context: html, text, full: html, text
  • src/hg/hgc/vcfClick.c - lines changed 11, context: html, text, full: html, text
  • src/hg/inc/vcfUi.h - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/vcfUi.c - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text

fd95861dbf3dd970c833b11076daa0da8738b1e8 Fri Mar 20 16:43:31 2020 -0700

• Adding 3 tracks derived from nextstrain.org: Nextstrain {Genes, Clades, Variants}. refs #25188
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/nextstrainNcov/doUpdate.sh - lines changed 52, context: html, text, full: html, text
  • src/hg/utils/otto/nextstrainNcov/makefile - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/otto/nextstrainNcov/nextstrain.py - lines changed 193, context: html, text, full: html, text
  • src/hg/utils/otto/nextstrainNcov/nextstrainClade.as - lines changed 19, context: html, text, full: html, text

720ff382be5d9492be9a896896185469f87de003 Fri Mar 20 17:01:33 2020 -0700

• Bump up priority of coronavirus Nextstrain tracks so they appear before RepeatMasker which doesn't really apply to viruses. refs #25188
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra - lines changed 2, context: html, text, full: html, text

ed72e3ea2e125d40211407d568a5daac06466d2e Fri Mar 20 17:04:39 2020 -0700

• Adding makeDb/doc note about Nexstrain tracks (otto) - refs #25188
  • src/hg/makeDb/doc/wuhCor1/initialBuild.txt - lines changed 3, context: html, text, full: html, text