Commits for angie

v456_base to v457_preview (2023-10-30 to 2023-11-06) v457

d6dd43ca0436bf894bafe00cc5ee1398e3ead0d0 Tue Oct 31 09:51:12 2023 -0700

• Removing a redundant hAllocConn that caused a 'Too many open sqlConnections for cache' test failure.
  • src/hg/lib/hgHgvs.c - lines changed 1, context: html, text, full: html, text

b7f10ba7db888f0fbaf5e49c7e42d7ad5291b1ac Tue Oct 31 09:52:22 2023 -0700

• More new lineages and a couple tweaks to old lineage paths.
  • src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 43, context: html, text, full: html, text

af90beb812e8f96e2283e62bd5082948ce455c58 Tue Oct 31 09:54:12 2023 -0700

• Updating default column offsets to match more recent nextclade versions
  • src/hg/utils/otto/sarscov2phylo/findDropoutContam.pl - lines changed 6, context: html, text, full: html, text

9fb2b35720b02cca3a9cece5cc8cdb782f86ed34 Tue Oct 31 09:56:35 2023 -0700

• Compress some previously uncompressed files so we don't waste quite so much disk space. Also spare sequences listed in sars-cov-2-variants/lineage-proposals repo file recombinants.tsv from the nextclade-based filters.
  • src/hg/utils/otto/sarscov2phylo/combineMetadata.sh - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/getCncb.sh - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/getCogUk.sh - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/getNcbi.sh - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh - lines changed 11, context: html, text, full: html, text

9a5ca254d03468faa1557b052349380a7067608e Tue Oct 31 09:57:03 2023 -0700

• Spare more sequences from the nextclade-based filters.
  • src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv - lines changed 11, context: html, text, full: html, text

aa0dc230ac3da4b9ba3ab771afb381397da71c05 Tue Oct 31 09:57:35 2023 -0700

• Use compressed CNCB fasta.
  • src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh - lines changed 1, context: html, text, full: html, text