Tweaked Makefile and using GetNextAlignment() in multiBamCov.

Makefile

@@ -77,5 +77,6 @@ all:
 clean:
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+	@rm -Rf $(BT_ROOT)/lib
 
 .PHONY: clean

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

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