9a49290fedc8b4f9c7a631dedcfe8ac3aa2b4cee
chinhli
  Thu Oct 20 14:10:43 2011 -0700
merge conflict resolved
diff --git src/lib/chainBlock.c src/lib/chainBlock.c
index 1b1e627..52dcb51 100644
--- src/lib/chainBlock.c
+++ src/lib/chainBlock.c
@@ -275,47 +275,45 @@
 if (branch->leaf == NULL)
     {
     if (dimCoord <= branch->cutCoord)
 	updateScoresOnWay(branch->lo, newDim, leaf);
     if (dimCoord >= branch->cutCoord)
 	updateScoresOnWay(branch->hi, newDim, leaf);
     }
 }
 
 static void findBestPredecessors(struct kdTree *tree, struct kdLeaf *leafList, 
 	ConnectCost connectCost, GapCost gapCost, void *gapData)
 /* Find best predecessor for each leaf. */
 {
 static struct predScore noBest;
 struct kdLeaf *leaf;
-struct kdLeaf *bestLeaf = NULL;
 double bestScore = 0;
 
 for (leaf = leafList; leaf != NULL; leaf = leaf->next)
     {
     struct predScore best;
     best = bestPredecessor(leaf, connectCost, gapCost, gapData, 0, tree->root, noBest);
     if (best.score > leaf->totalScore)
         {
 	leaf->totalScore = best.score;
 	leaf->bestPred = best.pred;
 	}
     updateScoresOnWay(tree->root, 0, leaf);
     if (bestScore < leaf->totalScore)
         {
 	bestScore = leaf->totalScore;
-	bestLeaf = leaf;
 	}
     }
 }
 
 static double scoreBlocks(struct cBlock *blockList, ConnectCost connectCost,
 	void *gapData)
 /* Score list of blocks including gaps between blocks. */
 {
 struct cBlock *block, *lastBlock = NULL;
 double score = 0;
 for (block = blockList; block != NULL; block = block->next)
     {
     score += block->score;
     if (lastBlock != NULL)
 	score -= connectCost(lastBlock, block, gapData);