--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/Makefile	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,70 @@
+CXX = g++
+CXXFLAGS= -Wall -O3 #-g #-std=c++11 #-Wall #-g
+#CXXFLAGS= -Wall -g #-std=c++11 #-Wall #-g
+LINKPATH= -I./samtools-0.1.19 -L./samtools-0.1.19
+LINKFLAGS = -lbam -lz -lm -lpthread 
+DEBUG=
+OBJECTS = stats.o subexon-graph.o 
+
+all: subexon-info combine-subexons classes vote-transcripts junc grader trust-splice add-genename addXS
+
+subexon-info: subexon-info.o $(OBJECTS)
+	if [ ! -f ./samtools-0.1.19/libbam.a ] ; \
+	        then \
+		                cd samtools-0.1.19 ; make ;\
+	fi ;
+	$(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) $(OBJECTS) subexon-info.o $(LINKFLAGS)
+
+combine-subexons: combine-subexons.o $(OBJECTS)
+	$(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) $(OBJECTS) combine-subexons.o $(LINKFLAGS)
+
+classes: classes.o constraints.o transcript-decider.o $(OBJECTS)
+	$(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) $(OBJECTS) constraints.o transcript-decider.o classes.o $(LINKFLAGS)
+
+trust-splice: trust-splice.o
+	$(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) $(OBJECTS) trust-splice.o $(LINKFLAGS)
+
+vote-transcripts: vote-transcripts.o 
+	$(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) $(OBJECTS) vote-transcripts.o $(LINKFLAGS)
+
+junc: junc.o
+	$(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) junc.o $(LINKFLAGS)
+
+grader: grader.o
+	$(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) grader.o $(LINKFLAGS)
+
+addXS: addXS.o
+	$(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) addXS.o $(LINKFLAGS)
+
+add-genename: add-genename.o
+	$(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) add-genename.o $(LINKFLAGS)
+
+subexon-info.o: SubexonInfo.cpp alignments.hpp blocks.hpp support.hpp defs.h stats.hpp
+	$(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
+combine-subexons.o: CombineSubexons.cpp alignments.hpp blocks.hpp support.hpp defs.h stats.hpp SubexonGraph.hpp
+	$(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
+stats.o: stats.cpp stats.hpp
+	$(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
+subexon-graph.o: SubexonGraph.cpp SubexonGraph.hpp 
+	$(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
+constraints.o: Constraints.cpp Constraints.hpp SubexonGraph.hpp alignments.hpp BitTable.hpp
+	$(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
+transcript-decider.o: TranscriptDecider.cpp TranscriptDecider.hpp Constraints.hpp BitTable.hpp
+	$(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
+classes.o: classes.cpp SubexonGraph.hpp SubexonCorrelation.hpp BitTable.hpp Constraints.hpp alignments.hpp TranscriptDecider.hpp
+	$(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
+trust-splice.o: GetTrustedSplice.cpp alignments.hpp
+	$(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
+vote-transcripts.o: Vote.cpp TranscriptDecider.hpp
+	$(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
+junc.o: FindJunction.cpp
+	$(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
+grader.o: grader.cpp
+	$(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
+addXS.o: AddXS.cpp
+	$(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
+add-genename.o: AddGeneName.cpp
+	$(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
+
+clean:
+	rm -f *.o *.gch subexon-info combine-subexons trust-splice vote-transcripts junc grader add-genename addXS