File Changes for angie

v405_preview to v405_preview2 (2020-09-21 to 2020-09-28) v405

• src/hg/hgTracks/vcfTrack.c
  • lines changed 107, context: html, text, full: html, text
    9174a163b341bfd2dd5c8fe84952265e74bef32a Sun Sep 27 23:50:14 2020 -0700
    Added setting sampleColorFile so one or more sample coloring schemes can be offered for the tree in VCF+tree tracks. refs #26177 TODO: document the new setting
• src/hg/inc/vcfUi.h
  • lines changed 2, context: html, text, full: html, text
    9174a163b341bfd2dd5c8fe84952265e74bef32a Sun Sep 27 23:50:14 2020 -0700
    Added setting sampleColorFile so one or more sample coloring schemes can be offered for the tree in VCF+tree tracks. refs #26177 TODO: document the new setting
• src/hg/lib/vcfUi.c
  • lines changed 47, context: html, text, full: html, text
    9174a163b341bfd2dd5c8fe84952265e74bef32a Sun Sep 27 23:50:14 2020 -0700
    Added setting sampleColorFile so one or more sample coloring schemes can be offered for the tree in VCF+tree tracks. refs #26177 TODO: document the new setting
• src/hg/makeDb/doc/wuhCor1/cladeLineageColors.pl
  • lines changed 122, context: html, text, full: html, text
    9174a163b341bfd2dd5c8fe84952265e74bef32a Sun Sep 27 23:50:14 2020 -0700
    Added setting sampleColorFile so one or more sample coloring schemes can be offered for the tree in VCF+tree tracks. refs #26177 TODO: document the new setting
• src/hg/makeDb/doc/wuhCor1/gisaidCladeColors.pl
  • lines changed 29, context: html, text, full: html, text
    9174a163b341bfd2dd5c8fe84952265e74bef32a Sun Sep 27 23:50:14 2020 -0700
    Added setting sampleColorFile so one or more sample coloring schemes can be offered for the tree in VCF+tree tracks. refs #26177 TODO: document the new setting
• src/hg/makeDb/doc/wuhCor1/phylogenetics.txt
  • lines changed 34, context: html, text, full: html, text
    9174a163b341bfd2dd5c8fe84952265e74bef32a Sun Sep 27 23:50:14 2020 -0700
    Added setting sampleColorFile so one or more sample coloring schemes can be offered for the tree in VCF+tree tracks. refs #26177 TODO: document the new setting
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    9174a163b341bfd2dd5c8fe84952265e74bef32a Sun Sep 27 23:50:14 2020 -0700
    Added setting sampleColorFile so one or more sample coloring schemes can be offered for the tree in VCF+tree tracks. refs #26177 TODO: document the new setting
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    9174a163b341bfd2dd5c8fe84952265e74bef32a Sun Sep 27 23:50:14 2020 -0700
    Added setting sampleColorFile so one or more sample coloring schemes can be offered for the tree in VCF+tree tracks. refs #26177 TODO: document the new setting
  • lines changed 51, context: html, text, full: html, text
    c7f2c6b539326f2478279bc17bd5869dad414d47 Mon Sep 28 09:34:47 2020 -0700
    Make separate release beta,public and release alpha versions of sarsCov2Phylo so that the new trackDb setting sampleColorFile is used only in alpha. Release tags should be moved along with the files that the setting points to. Setting will be ignored on beta/RR until v405 is rolled out. refs #26177
• src/hg/utils/faToVcf/faToVcf.c
  • lines changed 34, context: html, text, full: html, text
    0083ef3c88c18261d0cf52ec3259a1add58c9d8f Sun Sep 27 18:26:24 2020 -0700
    Added -noGenotypes option. Handle insertions in reference sequence. Don't count N bases in INFO column AN. refs MLQ #26227
• src/hg/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    a06dd1caf5a2f7992de5994e8e816c3f3006d788 Mon Sep 28 09:18:45 2020 -0700
    Add faToVcf to userApps -- used in an MLQ answer & I plan to add it to Data Access section of SARS-CoV-2 Phylogeny. refs #26227