Commits for angie

v396_base to v397_preview (2020-03-30 to 2020-04-06) v397

b5072af78461ac930024c95a8006a3e45c78afc0 Mon Mar 30 10:47:04 2020 -0700

• Updated with situation report links from Nextstrain's March 27 report. refs #25188
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainClade.html - lines changed 46, context: html, text, full: html, text

ac7cce26f5877b75218e08eec52eca476ddc33cc Mon Mar 30 14:52:32 2020 -0700

• Add per-clade subtracks to Nextstrain Vars for David. Also, Nextstrain changed ncov.json to use country instead of division for location. refs #25188
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra - lines changed 102, context: html, text, full: html, text
  • src/hg/utils/otto/nextstrainNcov/doUpdate.sh - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/otto/nextstrainNcov/nextstrain.py - lines changed 57, context: html, text, full: html, text
  • src/hg/utils/otto/nextstrainNcov/nextstrainClade.as - lines changed 2, context: html, text, full: html, text

306ef7620cf65cbd08a582f188fa49776d5ccd9d Mon Mar 30 15:36:49 2020 -0700

• Clarification suggested by Ana. refs #24695
  • src/hg/hgc/hgc.c - lines changed 1, context: html, text, full: html, text

e18fa442e05628a15efcad248c2f1c49b1e6c008 Tue Mar 31 10:03:17 2020 -0700

• Make casing consistent in hapCluster options. Thanks Brian L! refs #25197
  • src/hg/lib/vcfUi.c - lines changed 1, context: html, text, full: html, text

475424b5d722b4ff761681f1d3bd91ad666fb2d6 Wed Apr 1 10:17:03 2020 -0700

• For nested clades, add all clade samples to per-clade VCF. Also generate Newick (.nh) tree file and tweak sample name separator, in preparation for drawing the nextstrain tree in the VCF left label area. refs #25188
  • src/hg/utils/otto/nextstrainNcov/doUpdate.sh - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/otto/nextstrainNcov/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/nextstrainNcov/nextstrain.py - lines changed 45, context: html, text, full: html, text

4214801d5a5c31e35507528349985b90f86fcc6b Wed Apr 1 10:19:02 2020 -0700

• Tweak heights of nextstrain VCF tracks: 1. A2 and B are much larger since they include subclades; 2. Relative heights changed with latest data. refs #25188
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra - lines changed 8, context: html, text, full: html, text

0ee9c5c6fd7e6debb4e21c88139cb2ca19056565 Thu Apr 2 09:38:30 2020 -0700

• Install per-clade .nh tree files as well. refs #25188
  • src/hg/utils/otto/nextstrainNcov/doUpdate.sh - lines changed 2, context: html, text, full: html, text

74e378797b2f1b99b00d73f49c260bf5384cf670 Thu Apr 2 09:40:56 2020 -0700

• David noticed that nextstrainClade samples & counts weren't keeping up with change to VCF subtracks, so that nested clades include all descendants. Fixed. refs #25188
  • src/hg/utils/otto/nextstrainNcov/nextstrain.py - lines changed 27, context: html, text, full: html, text

578bb3e094f40c5273d594c38879c4e22b390e1a Thu Apr 2 09:46:23 2020 -0700

• Doh -- fixing incorrect bigDataUrl for nextstrainSamplesA3. refs #25188
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra - lines changed 1, context: html, text, full: html, text

0a9372ad1d6c6498fd3818a91edb65d932d890d9 Thu Apr 2 11:37:11 2020 -0700

• VCF: new option to display haplotypes ordered by a trackDb-specified Newick tree file. Tree is drawn in left label area. refs #25278
  • src/hg/hgTracks/vcfTrack.c - lines changed 301, context: html, text, full: html, text
  • src/hg/inc/vcfUi.h - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/vcfUi.c - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra - lines changed 12, context: html, text, full: html, text

04f62f226b0167adf59cc4b55980423164992934 Thu Apr 2 14:37:49 2020 -0700

• Fix bug that David H noticed in 'hapClusterMethod fileOrder' mode: depending on what tracks are viewed, sometimes sample labels were clipped instead of displayed. refs #25197
  • src/hg/hgTracks/vcfTrack.c - lines changed 14, context: html, text, full: html, text

5839fc5f68fc919fc61fad936929af799c52f577 Fri Apr 3 12:08:21 2020 -0700

• Add RGB colors to Nextstrain trees as fake branch lengths. Make hapClusterMethod treeFile use branch lengths as RGB colors. refs #25278
  • src/hg/hgTracks/vcfTrack.c - lines changed 15, context: html, text, full: html, text
  • src/hg/utils/otto/nextstrainNcov/nextstrain.py - lines changed 22, context: html, text, full: html, text

15e878a51d41f46c563209c95512fc23919ea5f3 Fri Apr 3 14:34:27 2020 -0700

• Little leap year bug (doesn't change any dates in output, but could by the end of 2020...). refs #25188
  • src/hg/utils/otto/nextstrainNcov/nextstrain.py - lines changed 2, context: html, text, full: html, text

dea7d848a3eb88f9521322b0d89650be3975d894 Sat Apr 4 13:44:50 2020 -0700

• Get rid of requirement for vcf track to have < 3000 genotypes in order to do haplotype display. Nextstrain is already up to 3365. refs #25188
  • src/hg/hgTracks/vcfTrack.c - lines changed 1, context: html, text, full: html, text