Commits for angie

v421_preview2 to v421_base (2021-09-20 to 2021-09-27) v421

724c2bc191aa30074eb93775ede264f38058d6bc Wed Sep 22 17:53:14 2021 -0700

• Always use -f (so reruns don't fail).
  • src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh - lines changed 2, context: html, text, full: html, text

4bfc83ad307e5017054b4852d17dc0b82f1997c5 Wed Sep 22 17:53:41 2021 -0700

• Better formatting of date mismatches for reporting to labs.
  • src/hg/utils/otto/sarscov2phylo/gbMetadataAddBioSample.pl - lines changed 2, context: html, text, full: html, text

6068fc9cbd3f8aa5f70f0535a5086423cf0c8d4c Wed Sep 22 20:42:55 2021 -0700

• Move the construction of new.masked.vcf.gz out of updateCombinedTree.sh into makeNewMaskedVcf.sh and move out the metadata stuff into combineMetadata.sh.
  • src/hg/utils/otto/sarscov2phylo/combineMetadata.sh - lines changed 113, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh - lines changed 287, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh - lines changed 335, context: html, text, full: html, text