Commits for angie
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v405_preview to v405_preview2 (2020-09-21 to 2020-09-28) v405
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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/faToVcf/faToVcf.c - 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/hgTracks/vcfTrack.c - lines changed 107, context: html, text, full: html, text
- src/hg/makeDb/doc/wuhCor1/cladeLineageColors.pl - lines changed 122, context: html, text, full: html, text
- src/hg/makeDb/doc/wuhCor1/gisaidCladeColors.pl - lines changed 29, context: html, text, full: html, text
- src/hg/makeDb/doc/wuhCor1/phylogenetics.txt - lines changed 34, context: html, text, full: html, text
- src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - 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
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/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 51, context: html, text, full: html, text
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