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Makefile.gcc
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Makefile.gcc
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#
# This file is part of the geneid distribution
# (c) by Roderic Guigo and Enrique Blanco, 2003
#
# Makefile for geneid
#
INCLUDE= ./include
CDIR= ./src
OBJ = ./objects
BIN = ./bin
HEADERS = $(INCLUDE)/geneid.h
PROGRAM= geneid
PRODUCT= $(BIN)/$(PROGRAM)
CC=gcc
#OPTS=-I$(INCLUDE) -Wall -O3
#OPTS=-I$(INCLUDE) -Wall -g
OPTS=-I$(INCLUDE) -std=c11 -ggdb -g3 -fvar-tracking-assignments -Wpedantic -Wall -Wextra -Wshadow -Wstrict-overflow -fno-strict-aliasing -Wdouble-promotion -Wundef -fno-common
## -fsanitize=address -fno-omit-frame-pointer
#######
OBJECTS = $(OBJ)/BackupGenes.o $(OBJ)/PeakEdgeScore.o $(OBJ)/GetTranscriptTermini-usingslopes.o $(OBJ)/BuildAcceptors.o $(OBJ)/BuildU12Acceptors.o $(OBJ)/BuildDonors.o \
$(OBJ)/BuildInitialExons.o $(OBJ)/BuildInternalExons.o $(OBJ)/BuildZeroLengthExons.o $(OBJ)/BuildUTRExons.o\
$(OBJ)/BuildORFs.o $(OBJ)/BuildSingles.o $(OBJ)/BuildSort.o $(OBJ)/BuildTerminalExons.o \
$(OBJ)/ComputeStopInfo.o $(OBJ)/CookingGenes.o $(OBJ)/CorrectExon.o \
$(OBJ)/Dictionary.o $(OBJ)/DumpHash.o $(OBJ)/FetchSequence.o \
$(OBJ)/GetSitesWithProfile.o $(OBJ)/GetStopCodons.o $(OBJ)/Output.o \
$(OBJ)/PrintExons.o $(OBJ)/PrintSites.o $(OBJ)/ReadExonsGFF.o \
$(OBJ)/ReadGeneModel.o $(OBJ)/ReadSequence.o $(OBJ)/ReadHSP.o $(OBJ)/RecomputePositions.o \
$(OBJ)/RequestMemory.o $(OBJ)/ProcessHSPs.o $(OBJ)/ScoreExons.o $(OBJ)/SearchEvidenceExons.o \
$(OBJ)/SetRatios.o $(OBJ)/SortExons.o $(OBJ)/SortSites.o $(OBJ)/SortHSPs.o $(OBJ)/SwitchFrames.o \
$(OBJ)/SwitchPositions.o $(OBJ)/Translate.o \
$(OBJ)/account.o $(OBJ)/beggar.o $(OBJ)/genamic.o $(OBJ)/manager.o \
$(OBJ)/readparam.o $(OBJ)/readargv.o \
#######
$(PRODUCT): $(BIN) $(OBJ) $(OBJ)/$(PROGRAM).o $(OBJECTS) $(HEADERS)
$(CC) $(OPTS) -o $(PRODUCT) $(OBJ)/$(PROGRAM).o $(OBJECTS) -lm
$(BIN) :
mkdir $(BIN);
$(OBJ) :
mkdir $(OBJ);
$(OBJ)/$(PROGRAM).o : $(CDIR)/$(PROGRAM).c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/$(PROGRAM).c -o $(OBJ)/$(PROGRAM).o
$(OBJ)/account.o : $(CDIR)/account.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/account.c -o $(OBJ)/account.o
$(OBJ)/beggar.o : $(CDIR)/beggar.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/beggar.c -o $(OBJ)/beggar.o
$(OBJ)/genamic.o : $(CDIR)/genamic.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/genamic.c -o $(OBJ)/genamic.o
$(OBJ)/manager.o : $(CDIR)/manager.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/manager.c -o $(OBJ)/manager.o
$(OBJ)/readargv.o : $(CDIR)/readargv.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/readargv.c -o $(OBJ)/readargv.o
$(OBJ)/readparam.o : $(CDIR)/readparam.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/readparam.c -o $(OBJ)/readparam.o
$(OBJ)/BackupGenes.o : $(CDIR)/BackupGenes.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/BackupGenes.c -o $(OBJ)/BackupGenes.o
$(OBJ)/GetTranscriptTermini-usingslopes.o : $(CDIR)/GetTranscriptTermini-usingslopes.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/GetTranscriptTermini-usingslopes.c -o $(OBJ)/GetTranscriptTermini-usingslopes.o
$(OBJ)/BuildAcceptors.o : $(CDIR)/BuildAcceptors.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/BuildAcceptors.c -o $(OBJ)/BuildAcceptors.o
$(OBJ)/BuildU12Acceptors.o : $(CDIR)/BuildU12Acceptors.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/BuildU12Acceptors.c -o $(OBJ)/BuildU12Acceptors.o
$(OBJ)/BuildDonors.o : $(CDIR)/BuildDonors.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/BuildDonors.c -o $(OBJ)/BuildDonors.o
#$(OBJ)/BuildU12Donors.o : $(CDIR)/BuildU12Donors.c $(HEADERS)
# $(CC) -c $(OPTS) $(CDIR)/BuildU12Donors.c -o $(OBJ)/BuildU12Donors.o
$(OBJ)/BuildInitialExons.o : $(CDIR)/BuildInitialExons.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/BuildInitialExons.c -o $(OBJ)/BuildInitialExons.o
$(OBJ)/BuildInternalExons.o : $(CDIR)/BuildInternalExons.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/BuildInternalExons.c -o $(OBJ)/BuildInternalExons.o
$(OBJ)/BuildZeroLengthExons.o : $(CDIR)/BuildZeroLengthExons.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/BuildZeroLengthExons.c -o $(OBJ)/BuildZeroLengthExons.o
$(OBJ)/BuildUTRExons.o : $(CDIR)/BuildUTRExons.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/BuildUTRExons.c -o $(OBJ)/BuildUTRExons.o
$(OBJ)/BuildORFs.o : $(CDIR)/BuildORFs.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/BuildORFs.c -o $(OBJ)/BuildORFs.o
$(OBJ)/BuildSingles.o : $(CDIR)/BuildSingles.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/BuildSingles.c -o $(OBJ)/BuildSingles.o
$(OBJ)/BuildSort.o: $(CDIR)/BuildSort.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/BuildSort.c -o $(OBJ)/BuildSort.o
$(OBJ)/BuildTerminalExons.o : $(CDIR)/BuildTerminalExons.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/BuildTerminalExons.c -o $(OBJ)/BuildTerminalExons.o
$(OBJ)/ComputeStopInfo.o : $(CDIR)/ComputeStopInfo.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/ComputeStopInfo.c -o $(OBJ)/ComputeStopInfo.o
$(OBJ)/CookingGenes.o: $(CDIR)/CookingGenes.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/CookingGenes.c -o $(OBJ)/CookingGenes.o
$(OBJ)/CorrectExon.o : $(CDIR)/CorrectExon.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/CorrectExon.c -o $(OBJ)/CorrectExon.o
$(OBJ)/Dictionary.o: $(CDIR)/Dictionary.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/Dictionary.c -o $(OBJ)/Dictionary.o
$(OBJ)/DumpHash.o: $(CDIR)/DumpHash.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/DumpHash.c -o $(OBJ)/DumpHash.o
$(OBJ)/FetchSequence.o : $(CDIR)/FetchSequence.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/FetchSequence.c -o $(OBJ)/FetchSequence.o
$(OBJ)/GetSitesWithProfile.o : $(CDIR)/GetSitesWithProfile.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/GetSitesWithProfile.c -o $(OBJ)/GetSitesWithProfile.o
$(OBJ)/GetStopCodons.o : $(CDIR)/GetStopCodons.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/GetStopCodons.c -o $(OBJ)/GetStopCodons.o
$(OBJ)/Output.o: $(CDIR)/Output.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/Output.c -o $(OBJ)/Output.o
$(OBJ)/PeakEdgeScore.o : $(CDIR)/PeakEdgeScore.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/PeakEdgeScore.c -o $(OBJ)/PeakEdgeScore.o
$(OBJ)/PrintExons.o : $(CDIR)/PrintExons.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/PrintExons.c -o $(OBJ)/PrintExons.o
$(OBJ)/PrintSites.o : $(CDIR)/PrintSites.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/PrintSites.c -o $(OBJ)/PrintSites.o
$(OBJ)/ProcessHSPs.o : $(CDIR)/ProcessHSPs.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/ProcessHSPs.c -o $(OBJ)/ProcessHSPs.o
$(OBJ)/ReadGeneModel.o: $(CDIR)/ReadGeneModel.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/ReadGeneModel.c -o $(OBJ)/ReadGeneModel.o
$(OBJ)/ReadExonsGFF.o : $(CDIR)/ReadExonsGFF.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/ReadExonsGFF.c -o $(OBJ)/ReadExonsGFF.o
$(OBJ)/ReadSequence.o : $(CDIR)/ReadSequence.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/ReadSequence.c -o $(OBJ)/ReadSequence.o
$(OBJ)/ReadHSP.o : $(CDIR)/ReadHSP.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/ReadHSP.c -o $(OBJ)/ReadHSP.o
$(OBJ)/RecomputePositions.o : $(CDIR)/RecomputePositions.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/RecomputePositions.c -o $(OBJ)/RecomputePositions.o
$(OBJ)/RequestMemory.o : $(CDIR)/RequestMemory.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/RequestMemory.c -o $(OBJ)/RequestMemory.o
$(OBJ)/ScoreExons.o : $(CDIR)/ScoreExons.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/ScoreExons.c -o $(OBJ)/ScoreExons.o
$(OBJ)/SearchEvidenceExons.o : $(CDIR)/SearchEvidenceExons.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/SearchEvidenceExons.c -o $(OBJ)/SearchEvidenceExons.o
$(OBJ)/SetRatios.o : $(CDIR)/SetRatios.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/SetRatios.c -o $(OBJ)/SetRatios.o
$(OBJ)/SortExons.o : $(CDIR)/SortExons.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/SortExons.c -o $(OBJ)/SortExons.o
$(OBJ)/SortSites.o : $(CDIR)/SortSites.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/SortSites.c -o $(OBJ)/SortSites.o
$(OBJ)/SortHSPs.o : $(CDIR)/SortHSPs.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/SortHSPs.c -o $(OBJ)/SortHSPs.o
$(OBJ)/SwitchFrames.o : $(CDIR)/SwitchFrames.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/SwitchFrames.c -o $(OBJ)/SwitchFrames.o
$(OBJ)/SwitchPositions.o : $(CDIR)/SwitchPositions.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/SwitchPositions.c -o $(OBJ)/SwitchPositions.o
$(OBJ)/Translate.o : $(CDIR)/Translate.c $(HEADERS)
$(CC) -c $(OPTS) $(CDIR)/Translate.c -o $(OBJ)/Translate.o
clean:
rm -f $(OBJ)/*.o $(PRODUCT) *~ $(INCLUDE)/*~ $(CDIR)/*~ core;
rmdir $(BIN) $(OBJ);