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1 CXX = g++
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2 CXXFLAGS= -Wall -O3 #-g #-std=c++11 #-Wall #-g
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3 #CXXFLAGS= -Wall -g #-std=c++11 #-Wall #-g
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4 LINKPATH= -I./samtools-0.1.19 -L./samtools-0.1.19
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5 LINKFLAGS = -lbam -lz -lm -lpthread
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6 DEBUG=
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7 OBJECTS = stats.o subexon-graph.o
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8
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9 all: subexon-info combine-subexons classes vote-transcripts junc grader trust-splice add-genename addXS
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10
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11 subexon-info: subexon-info.o $(OBJECTS)
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12 if [ ! -f ./samtools-0.1.19/libbam.a ] ; \
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13 then \
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14 cd samtools-0.1.19 ; make ;\
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15 fi ;
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16 $(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) $(OBJECTS) subexon-info.o $(LINKFLAGS)
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17
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18 combine-subexons: combine-subexons.o $(OBJECTS)
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19 $(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) $(OBJECTS) combine-subexons.o $(LINKFLAGS)
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20
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21 classes: classes.o constraints.o transcript-decider.o $(OBJECTS)
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22 $(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) $(OBJECTS) constraints.o transcript-decider.o classes.o $(LINKFLAGS)
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23
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24 trust-splice: trust-splice.o
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25 $(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) $(OBJECTS) trust-splice.o $(LINKFLAGS)
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26
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27 vote-transcripts: vote-transcripts.o
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28 $(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) $(OBJECTS) vote-transcripts.o $(LINKFLAGS)
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29
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30 junc: junc.o
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31 $(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) junc.o $(LINKFLAGS)
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32
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33 grader: grader.o
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34 $(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) grader.o $(LINKFLAGS)
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35
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36 addXS: addXS.o
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37 $(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) addXS.o $(LINKFLAGS)
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38
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39 add-genename: add-genename.o
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40 $(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) add-genename.o $(LINKFLAGS)
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41
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42 subexon-info.o: SubexonInfo.cpp alignments.hpp blocks.hpp support.hpp defs.h stats.hpp
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43 $(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
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44 combine-subexons.o: CombineSubexons.cpp alignments.hpp blocks.hpp support.hpp defs.h stats.hpp SubexonGraph.hpp
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45 $(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
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46 stats.o: stats.cpp stats.hpp
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47 $(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
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48 subexon-graph.o: SubexonGraph.cpp SubexonGraph.hpp
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49 $(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
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50 constraints.o: Constraints.cpp Constraints.hpp SubexonGraph.hpp alignments.hpp BitTable.hpp
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51 $(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
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52 transcript-decider.o: TranscriptDecider.cpp TranscriptDecider.hpp Constraints.hpp BitTable.hpp
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53 $(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
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54 classes.o: classes.cpp SubexonGraph.hpp SubexonCorrelation.hpp BitTable.hpp Constraints.hpp alignments.hpp TranscriptDecider.hpp
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55 $(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
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56 trust-splice.o: GetTrustedSplice.cpp alignments.hpp
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57 $(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
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58 vote-transcripts.o: Vote.cpp TranscriptDecider.hpp
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59 $(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
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60 junc.o: FindJunction.cpp
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61 $(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
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62 grader.o: grader.cpp
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63 $(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
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64 addXS.o: AddXS.cpp
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65 $(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
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66 add-genename.o: AddGeneName.cpp
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67 $(CXX) -c -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
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68
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69 clean:
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70 rm -f *.o *.gch subexon-info combine-subexons trust-splice vote-transcripts junc grader add-genename addXS
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