Commits for angie

ca41ef450e78c43619fcb96bfc6d8002fac95e32 Mon Oct 3 15:27:50 2022 -0700

Resolved more Ns to expected alleles. Added another bunch of new lineages for pango-designation v1.15.
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 218, context: html, text, full: html, text

cc1669639a750c73b05f85272a97129de52abae2 Mon Oct 10 15:40:06 2022 -0700

Don't limit search of dbDb.description to only terms starting with GC; instead, restrict search to the part within parentheses (skipping the assembly date) and restrict searches that would match too many institutions like Broad, WUGSC, Baylor, Agencourt unless people type in more letters of those. refs #30108
- src/hg/hgGateway/hgGateway.c - lines changed 19, context: html, text, full: html, text

541895c46dffc490e977491ac9361b49a8e9437f Mon Oct 10 15:42:43 2022 -0700

Add BA.5.1.29, BF.7.1, BA.5.3.5, and correct paths for XBC and XBC.1.
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 5, context: html, text, full: html, text

f35cefd3435d1513f3e130db211faa845068913a Mon Oct 10 15:43:36 2022 -0700

Move node for BA.2.75-masking back a few levels; add more sites, especially BA.2-level reversions.
- src/hg/utils/otto/sarscov2phylo/maskDelta.sh - lines changed 7, context: html, text, full: html, text

de878cd5e29e32002ebc64b66d7cf6989091f8ce Mon Oct 10 15:46:16 2022 -0700

Another regex tweak for fluff that ends up in GenBank names. Oh, those crazy [Hh]umans.
- src/hg/utils/otto/sarscov2phylo/fixNcbiFastaNames.pl - lines changed 1, context: html, text, full: html, text

9be0c7e4b3f76f5dcf979c2469e05b9ee20b2fab Mon Oct 10 15:47:00 2022 -0700

Adding recent recombinants that required explicit inclusion.
- src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv - lines changed 47, context: html, text, full: html, text

009620a961ec07ce597829ebac077d1920fae8f1 Mon Oct 10 15:47:58 2022 -0700

Loosen filtering parameters so we don't lop off XAW.
- src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh - lines changed 4, context: html, text, full: html, text

b81e6071edc73b0d973b29689c9d2dd6c84b8e8d Mon Oct 10 15:48:55 2022 -0700

Tighten -maxDiff since it is still a lot less stringent than the --max-path-length filtering applied after placement.
- src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh - lines changed 1, context: html, text, full: html, text

068a98d10ad734d52ac41951bd10dc4222952e67 Mon Oct 10 16:02:25 2022 -0700

Helper script for pango releases: put pip-compatible tarfiles in a staging directory for eventual hgdownload accessibility.
- src/hg/utils/otto/sarscov2phylo/makePangolinAssignmentRelease.sh - lines changed 64, context: html, text, full: html, text

871b54b7f7262469495a2db7bc064d3322ff9fa3 Wed Oct 12 13:45:51 2022 -0700

Auspice config: added entropy panel and filters for sample type, country, lineage/clade. HT @corneliusroemer
- src/hg/hgPhyloPlace/treeToAuspiceJson.c - lines changed 20, context: html, text, full: html, text

a384cc55ed66357a2e58c5d7a20f2125909b30b8 Wed Oct 12 14:32:51 2022 -0700

Parse ranges of IDs such as EPI_SET notation (EPI_ISL_1234-5678), requested by @corneliusroemer in https://github.com/yatisht/usher/issues/276
- src/hg/hgPhyloPlace/phyloPlace.c - lines changed 83, context: html, text, full: html, text

74b9ff8522c8be268456f80f8c8dbe8af73f447c Wed Oct 12 14:39:49 2022 -0700

Added two lineages that I should have added before v1.15 data release: BV.2 and BE.4.1.1. Added a bunch of recently designated lineages. Added BA.2.75.4_no9532 to fix problem with split BA.2.75.4. Added XA for easier comparison of two-letter lineages present in pango-designation vs. this file.
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 26, context: html, text, full: html, text

3a59fc70bda966dd32a5d17b00dfb6688ad40e28 Fri Oct 14 09:40:30 2022 -0700

NAR update reviewer feedback: make embedded tutorial video larger, no need to keep tiny default size.
- src/hg/hgPhyloPlace/hgPhyloPlace.c - lines changed 1, context: html, text, full: html, text

7cd88510c60532d95aee9e98ba02d191990d873e Sat Oct 15 20:34:05 2022 -0700

Fixing typo in corner case of writing alt alleles for VCF with imputed alleles, that caused segv when parsing the generated VCF. https://github.com/yatisht/usher/issues/282
- src/hg/hgPhyloPlace/writeCustomTracks.c - lines changed 1, context: html, text, full: html, text