a2a68e8ad4ff5927b604b27898c183a519c9e5f4 angie Tue Feb 23 20:08:34 2021 -0800 Instead of replacing small subtrees (usher -k) with the new single subtree option (-K), make both (unless a large number of sequences are uploaded; then just -K). diff --git src/hg/hgPhyloPlace/phyloPlace.h src/hg/hgPhyloPlace/phyloPlace.h index 481c747..79957c3 100644 --- src/hg/hgPhyloPlace/phyloPlace.h +++ src/hg/hgPhyloPlace/phyloPlace.h @@ -87,30 +87,31 @@ /* Parsed subtree from usher and derivative products. */ { struct subtreeInfo *next; struct tempName *subtreeTn; // Newick file from usher (may have condensed nodes) struct phyloTree *subtree; // Parsed subtree (#*** with annotated muts? shoudl we?_ struct hash *subtreeIdToIx; // Map of subtree nodes to VCF output sample order struct slName *subtreeUserSampleIds; // List of user-uploaded samples in this subtree struct slName *subtreeNameList; // List of leaf names with nicer names for cond. nodes }; struct usherResults /* Tree+samples download file, sample placements, and subtrees parsed from usher output. */ { struct tempName *bigTreePlusTn; // Newick file: original tree plus user's samples struct hash *samplePlacements; // Info about each sample's placement in the tree + struct subtreeInfo *singleSubtreeInfo; // Comprehensive subtree with all uploaded samples struct subtreeInfo *subtreeInfoList; // For each subtree: tree, file, node info etc. }; struct sampleMetadata /* Information about a virus sample. */ { char *strain; // Strain name, usually of the form Country/ArbitraryId/YYYY-MM-DD char *epiId; // GISAID EPI_ISL_[0-9]+ ID char *gbAcc; // GenBank accession char *date; // Sample collection date char *author; // Author(s) to credit char *nClade; // Nextstrain year-letter clade char *gClade; // GISAID amino acid change clade char *lineage; // Pangolin lineage char *country; // Country in which sample was collected