File Changes for angie

v462_base to v463_preview (2024-03-11 to 2024-03-18) v463

• src/hg/hgPhyloPlace/vcfFromFasta.c
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    6dfdf2e6277b1815d40117b0f1ff1508e6f92058 Fri Mar 15 13:41:09 2024 -0700
    Support for M. tuberculosis: at 4M bases, the genome is too large for arrays on the stack. Allocate & free instead.
• src/hg/hgPhyloPlace/writeCustomTracks.c
  • lines changed 6, context: html, text, full: html, text
    6dfdf2e6277b1815d40117b0f1ff1508e6f92058 Fri Mar 15 13:41:09 2024 -0700
    Support for M. tuberculosis: at 4M bases, the genome is too large for arrays on the stack. Allocate & free instead.
• src/hg/snp/dbSnpJsonToTab/dbSnpJsonToTab.c
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    b280493ca2969a1de7f3dd8322f49fac095e77ac Tue Mar 12 16:40:33 2024 -0700
    Call stripOldStudyVersions before addMissingRefAllele instead of after to avoid erroneous output when re-running on dbSnp 153 JSON. refs #33070 With this change, addMissingRefAllele is looking only at the latest version, and its added item does not get stripped back out due to having a default version of 0. Stripping the added ref allele back out caused downstream trouble in sortFrequencies; allele frequencies were lost, and then the Common subset included no indels (the variants that were missing ref alleles) for 153.
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
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    5ae4d83b976b96f74cc3e1846e525601b6473cb3 Fri Mar 15 13:43:16 2024 -0700
    Expand masked range for JN.1 after more discussion in cov-lineages/pango-designation#2510
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
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    6beb5b798df04141d3a69e5b80285e35d547fb4f Fri Mar 15 13:43:53 2024 -0700
    Adding more recombinants to exempt from filter.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    6b7815eee943235aa3fd850bf2ce4648755504d2 Fri Mar 15 13:42:16 2024 -0700
    More new lineages for pango-designation v1.26 and beyond.