diff --git a/Makefile b/Makefile
index 4abfdd2ad12901f4090b1b5cc67dc20f09136152..b12bb7df5de172c5008f35cf3a9a9de80af071a1 100644
--- a/Makefile
+++ b/Makefile
@@ -77,5 +77,6 @@ all:
 clean:
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+	@rm -Rf $(BT_ROOT)/lib
 
 .PHONY: clean
diff --git a/genomes/mouse.mm9.genome b/genomes/mouse.mm9.genome
index 84c1e72431d01f38c38346d7df191c1eefe0aa48..9c0955da583b8d0d00527596c6f919d722775366 100755
--- a/genomes/mouse.mm9.genome
+++ b/genomes/mouse.mm9.genome
@@ -7,7 +7,7 @@ chr6	149517037
 chr7	152524553
 chr8	131738871
 chr9	124076172
-chr10	129993255
+chr10 	129993255
 chr11	121843856
 chr12	121257530
 chr13	120284312
diff --git a/src/multiBamCov/multiBamCov.cpp b/src/multiBamCov/multiBamCov.cpp
index 3d53c8efca86ae3bb8bfd2308ebc2b006249baf0..e19b3c9f91a4847a7b66b2e9197fc7fdf20681ee 100644
--- a/src/multiBamCov/multiBamCov.cpp
+++ b/src/multiBamCov/multiBamCov.cpp
@@ -70,7 +70,7 @@ void MultiCovBam::CollectCoverage()
                     // everything checks out, just iterate through specified region, counting alignments
                     vector<int> counts(_bam_files.size());
                     BamAlignment al;
-                    while ( reader.GetNextAlignmentCore(al) )
+                    while ( reader.GetNextAlignment(al) )
                     {
                         // lookup the offset of the file name and tabulate coverage
                         // for the appropriate file