Commits for angie

v400_base to v401_preview (2020-06-22 to 2020-06-29) v401

606a508ff4d9eef9075418e54448edc89c35aae2 Tue Jun 23 13:38:04 2020 -0700

• Increase the max VCF track height to be more in line with the default maxItems-based maximumTrackHeight() (1000 items, 10px/item).
  • src/hg/lib/vcfUi.c - lines changed 1, context: html, text, full: html, text

60e8aef8f6340a0ec9f9432d6aa20ac526222fa4 Wed Jun 24 09:53:51 2020 -0700

• For the new hgwdev-demo-user machines, the USER passed in contains a hyphen which can't be part of a mysql table name (e.g. we need trackDb_demo_angie not trackDb_demo-angie), so replace it for table names.
  • src/hg/makeDb/trackDb/makefile - lines changed 8, context: html, text, full: html, text

8d050f7b9336a7d02c59240396f65f87efb3d3e4 Wed Jun 24 15:54:31 2020 -0700

• Update Nextstrain tracks to include new clade system. refs #25782
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainClade.html - lines changed 74, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainOldClade.html - lines changed 131, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainSamples.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainSamplesDevOnly.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainSamplesOldClades.html - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra - lines changed 247, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.v1.ra - lines changed 129, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 11, context: html, text, full: html, text

a0bf82e890e8668b06508a3d394ff85ea772b4aa Thu Jun 25 15:07:36 2020 -0700

• Typo fix
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainFreq.html - lines changed 1, context: html, text, full: html, text

062e6b7ae1ce485b7d4d048158c6c9a05780e9ea Thu Jun 25 15:08:27 2020 -0700

• Description for Nextstrain Parsimony track. refs #25799
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainParsimony.html - lines changed 83, context: html, text, full: html, text