827de614bca5613228664b8944048f61c61f336a
angie
  Fri Dec 2 09:44:45 2022 -0800
Use @yceh's new --existing_samples option to usher-sampled-server as a faster alternative to running matUtils.

diff --git src/hg/hgPhyloPlace/phyloPlace.c src/hg/hgPhyloPlace/phyloPlace.c
index 04db44b..0c23266 100644
--- src/hg/hgPhyloPlace/phyloPlace.c
+++ src/hg/hgPhyloPlace/phyloPlace.c
@@ -2964,32 +2964,32 @@
     }
 
 // Kick off child thread to load metadata simultaneously with running usher or matUtils.
 pthread_t *metadataPthread = mayStartLoaderPthread(metadataFile, loadMetadataWorker);
 
 struct usherResults *results = NULL;
 if (vcfTn)
     {
     fflush(stdout);
     results = runUsher(db, usherPath, protobufPath, vcfTn->forCgi, subtreeSize, &sampleIds,
                        treeChoices, &startTime);
     }
 else if (subtreesOnly)
     {
     char *matUtilsPath = getMatUtilsPath(TRUE);
-    results = runMatUtilsExtractSubtrees(matUtilsPath, protobufPath, subtreeSize,
-                                         sampleIds, &startTime);
+    results = runMatUtilsExtractSubtrees(db, matUtilsPath, protobufPath, subtreeSize,
+                                         sampleIds, treeChoices, &startTime);
     }
 
 struct hash *sampleMetadata = NULL;
 if (metadataPthread)
     {
     pthreadJoin(metadataPthread, (void **)(&sampleMetadata));
     reportTiming(&startTime, "wait for sample metadata loading thread to finish");
     }
 else
     {
     // We really need metadata -- load it the slow way.
     sampleMetadata = getSampleMetadata(metadataFile);
     reportTiming(&startTime, "load sample metadata without pthread");
     }