--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq-hts_1.0/mex/Makefile	Wed May 09 20:43:47 2012 -0400
@@ -0,0 +1,38 @@
+include ../bin/deseq_config.sh
+
+MEX=${MATLAB_MEX_PATH}
+MKOCTFILE=${OCTAVE_MKOCT}
+MATLAB_INCL=${MATLAB_INCLUDE_DIR}
+SAMDIR=${SAMTOOLS_DIR}
+
+
+all:	get_reads.mex get_bam_properties.mex interval_overlap.mex get_reads.mexa64 get_bam_properties.mexa64 interval_overlap.mexa64
+octave:	get_reads.mex get_bam_properties.mex interval_overlap.mex
+matlab:	get_reads.mexa64 get_bam_properties.mexa64 interval_overlap.mexa64
+
+
+get_reads.mexa64:	get_reads.cpp get_reads_direct.cpp mex_input.cpp read.cpp
+	rm -f *.o
+	${MEX} -g -O get_reads.cpp get_reads_direct.cpp mex_input.cpp read.cpp -I${SAMDIR} -L${SAMDIR} -lbam -lz -lcurses -I$(MATLAB_INCL)
+
+get_bam_properties.mexa64:	get_bam_properties.cpp
+	rm -f *.o
+	${MEX} -g -O get_bam_properties.cpp -I$(MATLAB_INCL)
+
+interval_overlap.mexa64:	interval_overlap.cpp
+	${MEX} -g -O interval_overlap.cpp -I$(MATLAB_INCL)
+
+get_reads.mex:	get_reads.cpp get_reads_direct.cpp mex_input.cpp read.cpp
+	rm -f *.o
+	${MKOCTFILE} -g --mex get_reads.cpp get_reads_direct.cpp mex_input.cpp read.cpp -I${SAMDIR} -L${SAMDIR} -lbam -lz -lcurses
+
+get_bam_properties.mex:	get_bam_properties.cpp
+	rm -f *.o
+	${MKOCTFILE} -g --mex get_bam_properties.cpp
+
+interval_overlap.mex: interval_overlap.cpp
+	rm -f *.o
+	${MKOCTFILE} -g --mex interval_overlap.cpp
+
+clean:	
+	rm -f *.o *.mexa64 *.mex