Commits for angie

v403_preview2 to v403_base (2020-08-17 to 2020-08-24) v403

7dfe7eaf228d1e26f812a9cfe811bd52cf60d9a9 Mon Aug 17 10:45:01 2020 -0700

• Add 'tableBrowser off' setting for Nextstrain Variants and SARS-CoV-2 Phylogeny at GISAID's request. refs #26072
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra - 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

7d992e15b156dca5c6601a989dc33a4bf229ce45 Thu Aug 20 10:14:08 2020 -0700

• Added support for highlightIds setting in VCF+treeFile custom tracks. refs #25943
  • src/hg/hgTracks/vcfTrack.c - lines changed 74, context: html, text, full: html, text

2ab977674ff8aa920d078fa3c8e263298de74529 Mon Aug 17 15:54:37 2020 -0700

• Prevent page from crashing just because the list of alts includes an IUPAC ambiguous character that vpGenomicToTranscript doesn't know how to deal with. Use alpha channel for the highlighted samples so they don't hide the vertical guidelines. refs #25943
  • src/hg/hgTracks/vcfTrack.c - lines changed 6, context: html, text, full: html, text

9b043c5143cff7efe24ec0f9baf61c71104acc5a Thu Aug 20 10:06:41 2020 -0700

• Allow SARS-CoV-2 VCF to use GenBank or RefSeq ID instead of our chromified RefSeq ID. (Russ request, no RM)
  • src/lib/linefile.c - lines changed 7, context: html, text, full: html, text
  • src/lib/vcf.c - lines changed 4, context: html, text, full: html, text

39b3ad00ec43efa3dbd5a8b0836d7a6a00776528 Wed Jul 29 13:28:23 2020 -0700

• Added vcfParseGenotypesGtOnly to speed up parsing when we have tens of thousands of genotype columns and just want the genotypes not any associated details. refs #25943
  • src/inc/vcf.h - lines changed 5, context: html, text, full: html, text
  • src/lib/vcf.c - lines changed 31, context: html, text, full: html, text

34ae341f397c44bda8ce0e2d59dcc3d18b5e519e Thu Aug 20 10:38:14 2020 -0700

• Use the new vcfParseGenotypesGtOnly for speed in haplotype displays.
  • src/hg/hgTracks/vcfTrack.c - lines changed 3, context: html, text, full: html, text

fa61094c53e0c3bb6a6ef2b8235c0744aeb5f7c3 Wed Jul 29 18:22:22 2020 -0700

• Tolerate extra stuff (such as whitespace) after the VCF version number in ##fileformat line. (no RM, Russ ran into trouble with it)
  • src/lib/vcf.c - lines changed 1, context: html, text, full: html, text