Commits for angie

827de614bca5613228664b8944048f61c61f336a Fri Dec 2 09:44:45 2022 -0800

Use @yceh's new --existing_samples option to usher-sampled-server as a faster alternative to running matUtils.
- src/hg/hgPhyloPlace/phyloPlace.c - lines changed 2, context: html, text, full: html, text
- src/hg/hgPhyloPlace/phyloPlace.h - lines changed 2, context: html, text, full: html, text
- src/hg/hgPhyloPlace/runUsher.c - lines changed 67, context: html, text, full: html, text

0598b71e08f7ce3db112b5a5fa4d5194a8435f5e Fri Dec 2 11:05:57 2022 -0800

Add more info to taxonium file, dump out list of samples in public tree.
- src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh - lines changed 5, context: html, text, full: html, text

0f91220571b0892ed4374511f992931de5d58fe8 Fri Dec 2 11:07:32 2022 -0800

Update regex to match Omicrons/recombinants.
- src/hg/utils/otto/sarscov2phylo/findDropoutContam.pl - lines changed 2, context: html, text, full: html, text

66463568b2220779915874153b9347a33af97f09 Fri Dec 2 11:08:40 2022 -0800

Increase maxAttempts, sometimes AWS is flaky but resolves.
- src/hg/utils/otto/sarscov2phylo/getCogUk.sh - lines changed 2, context: html, text, full: html, text

d80e5aa50badf8d4b1e0fbadfb5cd346b812d18e Fri Dec 2 11:09:52 2022 -0800

Remove outdated options from datasets command; don't waste time sleeping after final failure.
- src/hg/utils/otto/sarscov2phylo/getNcbi.sh - lines changed 5, context: html, text, full: html, text

89f7d08712d352128fc01e2688df63bb188fc56b Fri Dec 2 11:10:47 2022 -0800

Adding recent samples
- src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv - lines changed 59, context: html, text, full: html, text

b777f63dced2a62cdf363cc456ded46d569ceb46 Fri Dec 2 11:11:11 2022 -0800

Update nextclade output column indices
- src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh - lines changed 3, context: html, text, full: html, text

3ed65430d066888a23f7f97ebbc11eac3269586b Fri Dec 2 11:13:14 2022 -0800

Mask more UTR noisy positions in BA.2 onward.
- src/hg/utils/otto/sarscov2phylo/maskDelta.sh - lines changed 7, context: html, text, full: html, text

e442dc70425e6e5ec1220b81de6da8f60ae32703 Fri Dec 2 11:15:52 2022 -0800

New slew of lineages from v1.16 and beyond.
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 111, context: html, text, full: html, text

404482949921223c604b2361aeaa5d2e37b5d990 Fri Dec 2 11:17:57 2022 -0800

Use multiple cores in pangolin for cluster run -- the number of jobs per machine is limited by RAM.
- src/hg/utils/otto/sarscov2phylo/runPangolin.sh - lines changed 4, context: html, text, full: html, text

e66bfc81c03088103c395a9a09bda494be3e1132 Fri Dec 2 11:23:44 2022 -0800

Add more pruning before downsampling: sequences with two or more reversions relative to lineage root, and high mutation density branches. Add -P file to speed up reannotation on rerooted tree.
- src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh - lines changed 29, context: html, text, full: html, text

1b0eba97a41a2b733ce4a3b1998fe3cd264b3e08 Fri Dec 2 11:24:24 2022 -0800

Move 21L (BA.2) node back; add new clades 22E and 22F.
- src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv - lines changed 3, context: html, text, full: html, text

6b7b5c359f41944103a1209a09b076cdade0044b Fri Dec 2 11:25:11 2022 -0800

Add check for unannotated lineages.
- src/hg/utils/otto/sarscov2phylo/updatePublic.sh - lines changed 20, context: html, text, full: html, text

d4e0a5e68076aafa81d0852705fca8fe90fa19ac Fri Dec 2 15:23:04 2022 -0800

Avoid regex when looking for isolate component of each name in tree; just look for slashes and distance between them. When user uploads names, this saves ~40s.
- src/hg/hgPhyloPlace/phyloPlace.c - lines changed 12, context: html, text, full: html, text