Commits for angie

v455_base to v456_preview (2023-10-09 to 2023-10-16) v456

fde35693549abfb2a22a4846bebfac38abdd5522 Fri Oct 13 09:38:49 2023 -0700

• Use Ns for positions in pango-masked UTR regions.
  • src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 57, context: html, text, full: html, text

30d1e434dcd5b313f393eac770c8da2d4323d54f Fri Oct 13 11:45:13 2023 -0700

• Adding download & usher tree build scripts for several non-SARS-CoV-2 viruses. mpxv has been going for over a year, rsv & dengue for some months now. fluA is an incomplete work in progress, complicated by having 8 segments, greater distances, and different subtyping schemes for different segments and even for different types within the segments.
  • src/hg/utils/otto/dengue/buildTree.sh - lines changed 227, context: html, text, full: html, text
  • src/hg/utils/otto/dengue/getNcbiDengue.sh - lines changed 81, context: html, text, full: html, text
  • src/hg/utils/otto/fluA/buildTree.sh - lines changed 288, context: html, text, full: html, text
  • src/hg/utils/otto/fluA/getNcbiFluA.sh - lines changed 67, context: html, text, full: html, text
  • src/hg/utils/otto/fluA/splitGbff.pl - lines changed 22, context: html, text, full: html, text
  • src/hg/utils/otto/fluA/splitGbff.sh - lines changed 34, context: html, text, full: html, text
  • src/hg/utils/otto/mpxv/buildTree.sh - lines changed 166, context: html, text, full: html, text
  • src/hg/utils/otto/mpxv/getNcbiMpxv.sh - lines changed 109, context: html, text, full: html, text
  • src/hg/utils/otto/mpxv/mask.bb - 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/utils/otto/mpxv/mask.bed - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/otto/mpxv/mask.vcf.gz - 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/utils/otto/rsv/buildTree.sh - lines changed 314, context: html, text, full: html, text
  • src/hg/utils/otto/rsv/exclude.ids - lines changed 31, context: html, text, full: html, text
  • src/hg/utils/otto/rsv/getNcbiRsv.sh - lines changed 70, context: html, text, full: html, text
  • src/hg/utils/otto/rsv/goya.A.clade-mutations.tsv - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/otto/rsv/ramaekers.A.clade-mutations.tsv - lines changed 1, context: html, text, full: html, text