Commits for angie

v408_preview2 to v408_base (2020-11-30 to 2020-12-07) v408

ff5530a2dba0cbf6730cb36524ad2ce2fbc45adc Mon Nov 30 09:49:58 2020 -0800

• Add support for SARS-CoV-2 RefSeq or GenBank accesion in bam.
  • src/lib/bamFile.c - lines changed 14, context: html, text, full: html, text

fe68a3b72e3c63ac173d41a68122cb99a2a4f578 Mon Nov 30 16:41:55 2020 -0800

• David requests: point out that Nextstrain has drag-and-drop local private metadata display & link back to covid19.html landing page.
  • src/hg/hgPhyloPlace/hgPhyloPlace.c - lines changed 21, context: html, text, full: html, text

ce76a7bd0cd856b6cc1aa35360849af7fe224c45 Tue Dec 1 10:14:32 2020 -0800

• Another link & wording tweak suggested by David. Also update Nextstrain drag-and-drop link to new location.
  • src/hg/hgPhyloPlace/hgPhyloPlace.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/phyloPlace.h - lines changed 2, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/treeToAuspiceJson.c - lines changed 2, context: html, text, full: html, text

7c0d73b5b9eb8303ee04ba236d31a6703552581c Wed Dec 2 16:32:15 2020 -0800

• hgPhyloPlace metadata: add Nextstrain_clade and genbank_accession columns, refactor in prep for public data. * Move the metadatafile-reading code into phyloPlace.c so metadata file can be used for looking up lineage (no need for separate idToLineage file). * Support looking up metadata by GenBank ID in addition to EPI_ISL ID, in preparation for using protobuf and metadata from public sequences instead of GISAID.
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 157, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/phyloPlace.h - lines changed 27, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/treeToAuspiceJson.c - lines changed 136, context: html, text, full: html, text

f78b8c4c7e8c23acd998ce19c7ef5af7c404adc4 Wed Dec 2 16:54:28 2020 -0800

• Use Yatish's find_parsimonious_assignments program to make parsimony score bigWigs. Also save full output of find_parsimonious_assignments for collaborators (Russ request).
  • src/hg/utils/otto/sarscov2phylo/addUnmappedPublic.sh - lines changed 13, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/mapPublic.sh - lines changed 12, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/processRelease.sh - lines changed 25, context: html, text, full: html, text