81d541d9b6147b2a699ca84b2f450825fb489802
angie
  Mon Aug 16 15:23:18 2021 -0700
Removing -l (--retain-input-branch-lengths) option from usher because it causes all-0 lengths in subtrees (& wasn't necessary in the first place) -- reported to Russ by user.

diff --git src/hg/hgPhyloPlace/runUsher.c src/hg/hgPhyloPlace/runUsher.c
index 3052cf9..9689bd8 100644
--- src/hg/hgPhyloPlace/runUsher.c
+++ src/hg/hgPhyloPlace/runUsher.c
@@ -827,31 +827,31 @@
 
 struct usherResults *runUsher(char *usherPath, char *usherAssignmentsPath, char *vcfFile,
                               int subtreeSize, struct slName *userSampleIds,
                               struct hash *condensedNodes, int *pStartTime)
 /* Open a pipe from Yatish Turakhia's usher program, save resulting big trees and
  * subtrees to trash files, return list of slRef to struct tempName for the trash files
  * and parse other results out of stderr output. */
 {
 struct usherResults *results = usherResultsNew();
 char subtreeSizeStr[16];
 safef(subtreeSizeStr, sizeof subtreeSizeStr, "%d", subtreeSize);
 char *numThreadsStr = "16";
 struct tempName tnOutDir;
 trashDirFile(&tnOutDir, "ct", "usher_outdir", ".dir");
 char *cmd[] = { usherPath, "-v", vcfFile, "-i", usherAssignmentsPath, "-d", tnOutDir.forCgi,
-                "-k", subtreeSizeStr, "-K", SINGLE_SUBTREE_SIZE, "-T", numThreadsStr, "-u", "-l",
+                "-k", subtreeSizeStr, "-K", SINGLE_SUBTREE_SIZE, "-T", numThreadsStr, "-u",
                 NULL };
 char **cmds[] = { cmd, NULL };
 struct tempName tnStderr;
 trashDirFile(&tnStderr, "ct", "usher_stderr", ".txt");
 struct pipeline *pl = pipelineOpen(cmds, pipelineRead, NULL, tnStderr.forCgi);
 pipelineClose(&pl);
 reportTiming(pStartTime, "run usher");
 parseStderr(tnStderr.forCgi, results->samplePlacements);
 
 struct tempName *singleSubtreeTn = NULL, *subtreeTns[MAX_SUBTREES];
 struct variantPathNode *singleSubtreeMuts = NULL, *subtreeMuts[MAX_SUBTREES];
 int subtreeCount = processOutDirFiles(results, tnOutDir.forCgi, &singleSubtreeTn, &singleSubtreeMuts,
                                       subtreeTns, subtreeMuts, MAX_SUBTREES);
 if (singleSubtreeTn == NULL)
     {