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
@@ -1,40 +1,40 @@
 /* phyloPlace: place SARS-CoV-2 sequences in phylogenetic tree using add_missing_samples program. */
 
 /* Copyright (C) 2020 The Regents of the University of California */
 
 #include "common.h"
 #include "linefile.h"
 #include "options.h"
 #include "phyloPlace.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "phyloPlace - Place SARS-CoV-2 sequences in phylogenetic tree using add_missing_samples program\n"
   "usage:\n"
   "   phyloPlace file.[fa|vcf]\n"
   "options:\n"
   "   -subtreeSize=N               Value to pass to usher option --print-subtrees-size\n"
   );
 }
 
 /* Command line validation table. */
 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);
 }