2aa99ff0ca7a50af99ba59a3e8a54d7a819e7808
angie
  Thu Aug 26 12:30:42 2021 -0700
Yikes, I was forgetting to expand condensed nodes in the big tree when making custom track VCF for subtrees, resulting in some sequences not being found & having no alt alleles in VCF.

diff --git src/hg/hgPhyloPlace/phyloPlace.c src/hg/hgPhyloPlace/phyloPlace.c
index abe222f..6721f5c 100644
--- src/hg/hgPhyloPlace/phyloPlace.c
+++ src/hg/hgPhyloPlace/phyloPlace.c
@@ -2757,31 +2757,31 @@
     struct tempName *tsvTn = NULL, *sTsvTn = NULL;
     struct tempName *zipTn = makeSubtreeZipFile(results, jsonTns, singleSubtreeJsonTn,
                                                 &startTime);
     struct tempName *ctTn = NULL;
     if (subtreesOnly)
         {
         summarizeSubtrees(sampleIds, results, sampleMetadata, jsonTns, bigTree);
         reportTiming(&startTime, "describe subtrees");
         }
     else
         {
         findNearestNeighbors(results->samplePlacements, sampleMetadata, bigTree);
 
         // Make custom tracks for uploaded samples and subtree(s).
         struct phyloTree *sampleTree = NULL;
-        ctTn = writeCustomTracks(vcfTn, results, sampleIds, bigTree->tree,
+        ctTn = writeCustomTracks(vcfTn, results, sampleIds, bigTree,
                                  source, fontHeight, &sampleTree, &startTime);
 
         // Make a sample summary TSV file and accumulate S gene changes
         struct hash *spikeChanges = hashNew(0);
         tsvTn = writeTsvSummary(results, sampleTree, sampleIds, seqInfoList,
                                                  geneInfoList, gSeqWin, spikeChanges, &startTime);
         sTsvTn = writeSpikeChangeSummary(spikeChanges, slCount(sampleIds));
         downloadsRow(results->bigTreePlusTn->forHtml, tsvTn->forHtml, sTsvTn->forHtml,
                      zipTn->forHtml);
 
         int seqCount = slCount(seqInfoList);
         if (seqCount <= MAX_SEQ_DETAILS)
             {
             summarizeSequences(seqInfoList, isFasta, results, jsonTns, sampleMetadata, refGenome);
             reportTiming(&startTime, "write summary table (including reading in lineages)");