Commits for angie

v408_base to v409_preview (2020-12-07 to 2021-01-04) v409

cd9c54f4262db97f1c9201411a0d84460de87690 Thu Dec 3 15:30:13 2020 -0800

• Try harder to look up sample metadata in the absence of EPI or GenBank acc: if name from protobuf is name|id|... then look up name and id.
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 11, context: html, text, full: html, text

bba5c10004bdcf6538a2d3ea07e7542eada31e0e Thu Dec 3 15:32:07 2020 -0800

• Don't overwrite name from protobuf with strain name; not necessary and loses info about condensed nodes.
  • src/hg/hgPhyloPlace/treeToAuspiceJson.c - lines changed 3, context: html, text, full: html, text

f2690b5f40e7e33dc355782853e812c76f4736ea Fri Dec 4 09:11:41 2020 -0800

• Add minimal metadata file for public sequences for use by hgPhyloPlace.
  • src/hg/utils/otto/sarscov2phylo/mapPublic.sh - lines changed 22, context: html, text, full: html, text

b7c2dcc865207dd23298429f93057c9068acef68 Wed Dec 9 15:48:34 2020 -0800

• hgPhyloPlace: Add config option treeChoices: tab-sep file of {protobuf, metadata, source, description} so we can offer the user a choice between GISAID and public sequence trees (possibly different releases for reproducibility).
  • src/hg/hgPhyloPlace/hgPhyloPlace.c - lines changed 18, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 90, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/phyloPlace.h - lines changed 19, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/phyloPlaceMain.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/treeToAuspiceJson.c - lines changed 14, context: html, text, full: html, text

0018392edd796d5e02beecaf8482e3e905d9ef94 Thu Dec 10 09:47:54 2020 -0800

• Nextstrain clades now include subclades; for now, ignore subclades for coloring.
  • src/hg/utils/otto/sarscov2phylo/cladeLineageColors.pl - lines changed 3, context: html, text, full: html, text

70e001e0f7a71f53c7a70b45feabac07d9d3751b Mon Dec 14 16:35:16 2020 -0800

• Update sarscov2phylo process to use tree and multi-seq ali's downloaded from GISAID instead of tree from github and aligning nextfasta locally.
  • src/hg/utils/otto/sarscov2phylo/extractUnmappedPublic.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/mapPublic.sh - lines changed 19, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/processGisaid.sh - lines changed 150, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/updateSarsCov2Phylo.sh - lines changed 9, context: html, text, full: html, text

b89ddcc7f8d37a686a917fd22a321b963821dfa5 Mon Dec 14 16:37:58 2020 -0800

• Added -veryDetailed option to show not only size, but also #Ns in each sequence.
  • src/utils/faSize/faSize.c - lines changed 10, context: html, text, full: html, text

7124216a15d1239d897a2cc77888ff8640bd207c Mon Dec 14 17:05:04 2020 -0800

• Automate linking of sarsCov2Phylo and sarsCov2PhyloPub /gbdb/ files.
  • src/hg/utils/otto/sarscov2phylo/installSarsCov2Phylo.sh - lines changed 80, context: html, text, full: html, text