Commits for angie

v407_preview2 to v407_base (2020-11-09 to 2020-11-16) v407

f501def66bb2db196a4ada2a7eff65d03af33171 Wed Nov 11 10:12:45 2020 -0800

• New util vcfFilter for SARS-CoV-2 work; expects monoploid genotypes, would need extension for diploid.
  • src/utils/vcfFilter/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/vcfFilter/tests/expected/testMinAc1Gt.vcf - lines changed 88, context: html, text, full: html, text
  • src/utils/vcfFilter/tests/expected/testMinAc1GtExclude.vcf - lines changed 85, context: html, text, full: html, text
  • src/utils/vcfFilter/tests/expected/testMinAc1NoGt.vcf - lines changed 98, context: html, text, full: html, text
  • src/utils/vcfFilter/tests/expected/testMinAc2RenameGt.vcf - lines changed 18, context: html, text, full: html, text
  • src/utils/vcfFilter/tests/expected/testRenameGt.vcf - lines changed 98, context: html, text, full: html, text
  • src/utils/vcfFilter/tests/expected/testRenameNoGt.vcf - lines changed 98, context: html, text, full: html, text
  • src/utils/vcfFilter/tests/input/exclude.vcf - lines changed 14, context: html, text, full: html, text
  • src/utils/vcfFilter/tests/input/subset.vcf - lines changed 98, context: html, text, full: html, text
  • src/utils/vcfFilter/tests/makefile - lines changed 37, context: html, text, full: html, text
  • src/utils/vcfFilter/vcfFilter.c - lines changed 376, context: html, text, full: html, text

8423ff7c26baa30c51e490ded78c8d97a197076a Wed Nov 11 10:16:01 2020 -0800

• Adding vcfFilter to top-level build, but not as a public util at this time because it assumes monoploid genotypes.
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text

d6620ab7a89bf7c2779d5bebe836fe7850ca832a Wed Nov 11 14:43:06 2020 -0800

• Updating RefSeq accession version.
  • src/hg/lib/tests/expected/hgvs/validTerms.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/tests/input/hgvs/validTerms.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/hgvsToVcf/tests/expected/clinVarChanges.vcf - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/hgvsToVcf/tests/input/clinVarChanges.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab - lines changed 16, context: html, text, full: html, text

f75874a85e09a19a652ca8c06cd72be5fba5482f Thu Nov 12 08:59:08 2020 -0800

• Added section about hgPhyloPlace/UShER to CoViD-19 landing page. refs #26516
  • src/hg/htdocs/covid19.html - lines changed 49, context: html, text, full: html, text
  • src/hg/htdocs/images/covid19/UShER_example.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/htdocs/images/covid19/usher_logo.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)