b7c2dcc865207dd23298429f93057c9068acef68
angie
  Wed Dec 9 15:48:34 2020 -0800
hgPhyloPlace: Add config option treeChoices: tab-sep file of {protobuf, metadata, source, description} so we can offer the user a choice between GISAID and public sequence trees (possibly different releases for reproducibility).

diff --git src/hg/hgPhyloPlace/phyloPlaceMain.c src/hg/hgPhyloPlace/phyloPlaceMain.c
index 5e22e50..be7310f 100644
--- src/hg/hgPhyloPlace/phyloPlaceMain.c
+++ src/hg/hgPhyloPlace/phyloPlaceMain.c
@@ -23,18 +23,18 @@
 static struct optionSpec options[] = {
     { "subtreeSize", OPTION_INT },
     {NULL, 0},
 };
 
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 2)
     usage();
 char *userSeqOrVcf = argv[1];
 struct lineFile *lf = lineFileOpen(userSeqOrVcf, TRUE);
 int subtreeSize = optionInt("subtreeSize", 50);
-char *ctFile = phyloPlaceSamples(lf, "wuhCor1", TRUE, subtreeSize, 9);
+char *ctFile = phyloPlaceSamples(lf, "wuhCor1", NULL, TRUE, subtreeSize, 9);
 return (ctFile == NULL);
 }