644e660c5f6db00acf08433f9a7ed09738e13488
braney
  Sun Mar 8 18:57:44 2015 -0700
add a menu in hgTracksUi to let folks choose a coalescent ancestor when
resolving duplications (per Joel)

diff --git src/hg/hgTracks/snakeTrack.c src/hg/hgTracks/snakeTrack.c
index 6125f9a..1f12abb 100644
--- src/hg/hgTracks/snakeTrack.c
+++ src/hg/hgTracks/snakeTrack.c
@@ -1200,31 +1200,34 @@
 struct errCatch *errCatch = errCatchNew();
 if (errCatchStart(errCatch))
     {
     char *fileName = trackDbSetting(tg->tdb, "bigDataUrl");
     char *otherSpecies = trackDbSetting(tg->tdb, "otherSpecies");
     char *errString;
     int handle = halOpenLOD(fileName, &errString);
     if (handle < 0)
 	warn("HAL open error: %s\n", errString);
     boolean isPackOrFull = (tg->visibility == tvFull) || 
 	(tg->visibility == tvPack);
     hal_dup_type_t dupMode =  (isPackOrFull) ? HAL_QUERY_AND_TARGET_DUPS :
 	HAL_QUERY_DUPS;
     hal_seqmode_type_t needSeq = isPackOrFull && (winBaseCount < showSnpWidth) ? HAL_LOD0_SEQUENCE : HAL_NO_SEQUENCE;
     int mapBackAdjacencies = (tg->visibility == tvFull);
-    struct hal_block_results_t *head = halGetBlocksInTargetRange(handle, otherSpecies, trackHubSkipHubName(database), chromName, winStart, winEnd, 0, needSeq, dupMode,mapBackAdjacencies, &errString);
+    char codeVarName[1024];
+    safef(codeVarName, sizeof codeVarName, "%s.coalescent", tg->tdb->track);
+    char *coalescent = cartOptionalString(cart, codeVarName);
+    struct hal_block_results_t *head = halGetBlocksInTargetRange(handle, otherSpecies, trackHubSkipHubName(database), chromName, winStart, winEnd, 0, needSeq, dupMode,mapBackAdjacencies, coalescent, &errString);
 
     // did we get any blocks from HAL
     if (head == NULL)
 	{
 	warn("HAL get blocks error: %s\n", errString);
 	errCatchEnd(errCatch);
 	return;
 	}
     struct hal_block_t* cur = head->mappedBlocks;
     struct linkedFeatures *lf = NULL;
     struct hash *qChromHash = newHash(5);
     struct linkedFeatures *lfList = NULL;
     char buffer[4096];
 
 #ifdef NOTNOW