The Makefile should be modified

[xieduo7]

There should be $(BAMTOOLS_ROOT)/include/bamtools instead of $(BAMTOOLS_ROOT)/include:

Rseq_bam_stats:
	@mkdir -p $(PREFIX)/$(BIN)
	@echo "* compiling" $(SOURCE_STA)
	@$(CXX) $(SRC)/$(SOURCE_STA) -o $(PREFIX)/$(BIN)/$(STA) $(BAMFLAGS) $(CXXFLAGS) $(LBFLAGS) $(BOOSTFLAGS) -I $(BAMTOOLS_ROOT)/include/bamtools -I $(ZLIB_ROOT)/include/ -I $(BOOST_ROOT)/include/ -L $(BAMTOOLS_ROOT)/lib/ -L $(ZLIB_ROOT)/lib/ -L $(BOOST_ROOT)/lib/

mappingFlankingVariants:
	@echo "* compiling" $(SOURCE_MFV)
	@$(CXX) $(SRC)/$(SOURCE_MFV) -o $(PREFIX)/$(BIN)/$(MFV) $(BAMFLAGS) $(CXXFLAGS) $(LBFLAGS) $(BOOSTFLAGS) -I $(BAMTOOLS_ROOT)/include/bamtools -I $(ZLIB_ROOT)/include/ -I $(BOOST_ROOT)/include/ -L $(BAMTOOLS_ROOT)/lib/ -L $(ZLIB_ROOT)/lib/ -L $(BOOST_ROOT)/lib/

novelSnvFilter_ACGT:
	@echo "* compiling" $(SOURCE_REC)
	@$(CXX) $(SRC)/$(SOURCE_REC) -o $(PREFIX)/$(BIN)/$(REC) $(BAMFLAGS) $(CXXFLAGS) $(LBFLAGS) $(BOOSTFLAGS) -I $(BAMTOOLS_ROOT)/include/bamtools -I $(ZLIB_ROOT)/include/ -I $(BOOST_ROOT)/include/ -L $(BAMTOOLS_ROOT)/lib/ -L $(ZLIB_ROOT)/lib/ -L $(BOOST_ROOT)/lib/

grep_starts:
	@echo "* compiling" $(SOURCE_GS)
	@$(CXX) $(SRC)/$(SOURCE_GS) -o $(PREFIX)/$(BIN)/$(GS) $(BAMFLAGS) $(CXXFLAGS) $(LBFLAGS) $(BOOSTFLAGS) -I $(BAMTOOLS_ROOT)/include/bamtools -I $(ZLIB_ROOT)/include/ -I $(BOOST_ROOT)/include/ -L $(BAMTOOLS_ROOT)/lib/ -L $(ZLIB_ROOT)/lib/ -L $(BOOST_ROOT)/lib/

If not, it will report error:

novelSnvFilter_ACGT.cpp:14:10: fatal error: api/BamReader.h: No such file or directory
   14 | #include <api/BamReader.h>
      |          ^~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [Makefile:37: novelSnvFilter_ACGT] Error 1

Best,
Duo