e14c2761ca01d8175578df87bd5311b5c0442bfb
angie
  Thu Nov 19 13:04:01 2020 -0800
New CGI hgPhyloPlace: place SARS-CoV-2 genomes in fasta or VCF on phylogenetic tree using Yatish Turakhia's UShER program; add subtree custom tracks and Nextstrain linkouts to visualize results.  refs #25943

diff --git src/hg/hgPhyloPlace/phyloPlaceMain.c src/hg/hgPhyloPlace/phyloPlaceMain.c
new file mode 100644
index 0000000..5e22e50
--- /dev/null
+++ src/hg/hgPhyloPlace/phyloPlaceMain.c
@@ -0,0 +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);
+return (ctFile == NULL);
+}