08ec019f344fc52bd83ea3a98bedccd0048d732c
angie
  Mon May 24 00:04:08 2021 -0700
Let the user upload a file containing names or IDs of sequences already in the selected tree; run matUtils extract to get subtrees that include those sequences.  protobufs.tab gets a new optional column to specify a file that maps alias to tree name/ID (e.g. for mapping EPI_ISL to public names/IDs).

diff --git src/hg/hgPhyloPlace/phyloPlaceMain.c src/hg/hgPhyloPlace/phyloPlaceMain.c
index be7310f..57e12f8 100644
--- src/hg/hgPhyloPlace/phyloPlaceMain.c
+++ src/hg/hgPhyloPlace/phyloPlaceMain.c
@@ -23,18 +23,23 @@
 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", NULL, TRUE, subtreeSize, 9);
-return (ctFile == NULL);
+boolean success = FALSE;
+char *ctFile = phyloPlaceSamples(lf, "wuhCor1", NULL, TRUE, subtreeSize, 9, &success);
+if (ctFile)
+    printf("ctFile = %s\n", ctFile);
+else
+    printf("no ctFile.\n");
+return (success == TRUE);
 }