55d15bfd5b19c9755b8385df51cd002a61e2baf6 angie Mon Jan 4 18:04:38 2021 -0800 When writing custom tracks, attribute public vs. GISAID sequences correctly. diff --git src/hg/hgPhyloPlace/phyloPlace.c src/hg/hgPhyloPlace/phyloPlace.c index 79dc952..2a44636 100644 --- src/hg/hgPhyloPlace/phyloPlace.c +++ src/hg/hgPhyloPlace/phyloPlace.c @@ -1619,31 +1619,31 @@ else if (subtreeCount > 1) printf("Unrelated sample"); printf("</h3>\n"); makeNextstrainButton("viewNextstrainSub", ix, jsonTns); puts("<br>"); // Make a sub-subtree with only user samples for display: struct phyloTree *subtree = phyloOpenTree(ti->subtreeTn->forCgi); subtree = phyloPruneToIds(subtree, ti->subtreeUserSampleIds); describeSamplePlacements(ti->subtreeUserSampleIds, results->samplePlacements, subtree, sampleMetadata, bigTree, source); } reportTiming(&startTime, "describe placements"); // Make custom tracks for uploaded samples and subtree(s). struct tempName *ctTn = writeCustomTracks(vcfTn, results, sampleIds, bigTree->tree, - fontHeight, &startTime); + source, fontHeight, &startTime); // Offer big tree w/new samples for download puts("<h3>Downloads</h3>"); puts("<ul>"); printf("<li><a href='%s' download>SARS-CoV-2 phylogenetic tree " "with your samples (Newick file)</a>\n", results->bigTreePlusTn->forHtml); for (ix = 0, ti = results->subtreeInfoList; ti != NULL; ti = ti->next, ix++) { printf("<li><a href='%s' download>Subtree with %s", ti->subtreeTn->forHtml, ti->subtreeUserSampleIds->name); struct slName *sln; for (sln = ti->subtreeUserSampleIds->next; sln != NULL; sln = sln->next) printf(", %s", sln->name); puts(" (Newick file)</a>"); printf("<li><a href='%s' download>Auspice JSON for subtree with %s",