Commits for angie

v415_preview2 to v415_base (2021-05-17 to 2021-05-24) v415

b4339e1d0387e40589c2e1f16727f8f1d882cd1e Wed May 19 09:32:32 2021 -0700

• faToVcf: when sequences aren't the expected size, mention that non-IUPAC chars are silently ignored since that's a common cause with non-UCSC-processed seqs.
  • src/hg/utils/faToVcf/faToVcf.c - lines changed 3, context: html, text, full: html, text

bdc1ddd9389c69f90464e15fff6661b52befdd1c Sun May 23 13:49:32 2021 -0700

• If a sequence can't be aligned to the reference then move it from filteredSeqs to failedSeqs so it doesn't end up in the VCF with no actual calls.
  • src/hg/hgPhyloPlace/vcfFromFasta.c - lines changed 36, context: html, text, full: html, text

08ec019f344fc52bd83ea3a98bedccd0048d732c Mon May 24 00:04:08 2021 -0700

• Let the user upload a file containing names or IDs of sequences already in the selected tree; run matUtils extract to get subtrees that include those sequences. protobufs.tab gets a new optional column to specify a file that maps alias to tree name/ID (e.g. for mapping EPI_ISL to public names/IDs).
  • src/hg/hgPhyloPlace/hgPhyloPlace.c - lines changed 11, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 323, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/phyloPlace.h - lines changed 16, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/phyloPlaceMain.c - lines changed 7, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/runUsher.c - lines changed 40, context: html, text, full: html, text

81f19001a612343bae377e1df72facad1c5e3197 Mon May 24 00:06:17 2021 -0700

• Updating description to clarify how representative sequences were downloaded from GISAID. refs MLQ #27590
  • src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.html - lines changed 20, context: html, text, full: html, text

3547a31b1b15f488d80771ed1af98b0e37def648 Mon May 24 09:54:02 2021 -0700

• Minor wording tweak.
  • src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.html - lines changed 2, context: html, text, full: html, text