File Changes for angie

v455_preview2 to v455_base (2023-10-02 to 2023-10-09) v455

• src/hg/htdocs/goldenPath/help/vcf.html
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    5d880eccee6e7beee8e1896931bba081883ac0a3 Wed Oct 4 09:04:29 2023 -0700
    Replace spaces with tabs in #CHROM header line of example VCF.
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
  • lines changed 4, context: html, text, full: html, text
    5793028c4b37b6cb8300580e70d7b078abc516b2 Wed Oct 4 17:46:58 2023 -0700
    Mask deletion 21991-21993 in XBB.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
  • lines changed 3, context: html, text, full: html, text
    afedd6d0dae5767b8ee9041119d72a65360f77e0 Wed Oct 4 17:46:28 2023 -0700
    Strip stuff past the accession in headers when making fasta for pangolin.
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
  • lines changed 34, context: html, text, full: html, text
    dc2399eba0ad110c5df9658b67da773e302b3bb0 Wed Oct 4 17:47:39 2023 -0700
    More requested exceptions to filters, thanks @aviczhl2.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 95, context: html, text, full: html, text
    9ddf9825cc02b849ed222d5a1274e4c385ba599b Wed Oct 4 17:45:17 2023 -0700
    Added new lineages and updated some existing ones.
• src/hg/utils/otto/sarscov2phylo/updatePublic.sh
  • lines changed 2, context: html, text, full: html, text
    87d8340f2b3cdce33de9043c4ecd9afdfef55b25 Wed Oct 4 17:48:43 2023 -0700
    Set prevDate at the beginning so we don't run into trouble for occasional epic long downloads from CNCB.