###
### This file is generated automatically.  DO NOT MODIFY BY HAND!
###

aligns/KmerAlignCore.o: $(SRC)/aligns/KmerAlignCore.cc $(SRC)/aligns/KmerAlignCore.h $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/util/mutil.h 
analysis/AACodons.o: $(SRC)/analysis/AACodons.cc $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/util/mutil.h 
analysis/BreakTransByPairs.o: $(SRC)/aligns/KmerAlignCore.h $(SRC)/analysis/AACodons.h $(SRC)/analysis/BreakTransByPairs.cc $(SRC)/analysis/DNAVector.h $(SRC)/analysis/KmerTable.h $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h 
analysis/Chrysalis.o: $(SRC)/analysis/AACodons.h $(SRC)/analysis/Chrysalis.cc $(SRC)/analysis/CompMgr.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/TranscriptomeGraph.h $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h 
analysis/DNAVector.o: $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.cc $(SRC)/analysis/DNAVector.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/util/mutil.h 
analysis/DeBruijnGraph.o: $(SRC)/analysis/DeBruijnGraph.cc $(SRC)/analysis/DeBruijnGraph.h $(SRC)/analysis/sequenceUtil.h $(SRC)/analysis/string_util.h 
analysis/GraphFromFasta.o: $(SRC)/aligns/KmerAlignCore.h $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/DeBruijnGraph.h $(SRC)/analysis/GraphFromFasta.cc $(SRC)/analysis/KmerTable.h $(SRC)/analysis/NonRedKmerTable.h $(SRC)/analysis/sequenceUtil.h $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h 
analysis/IsoformAugment.o: $(SRC)/aligns/KmerAlignCore.h $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/IsoformAugment.cc $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h 
analysis/JoinTransByPairs.o: $(SRC)/aligns/KmerAlignCore.h $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/JoinTransByPairs.cc $(SRC)/analysis/KmerTable.h $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h 
analysis/KmerTable.o: $(SRC)/aligns/KmerAlignCore.h $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/KmerTable.cc $(SRC)/analysis/KmerTable.h $(SRC)/analysis/NonRedKmerTable.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/util/mutil.h 
analysis/NonRedKmerTable.o: $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/NonRedKmerTable.cc $(SRC)/analysis/NonRedKmerTable.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/util/mutil.h 
analysis/QuantifyGraph.o: $(SRC)/aligns/KmerAlignCore.h $(SRC)/analysis/AACodons.h $(SRC)/analysis/CompMgr.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/KmerTable.h $(SRC)/analysis/QuantifyGraph.cc $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h 
analysis/ReadsToTranscripts.o: $(SRC)/analysis/AACodons.h $(SRC)/analysis/CompMgr.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/NonRedKmerTable.h $(SRC)/analysis/ReadsToTranscripts.cc $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h 
analysis/RunButterfly.o: $(SRC)/analysis/RunButterfly.cc $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h 
analysis/TranscriptomeFromVaryK.o: $(SRC)/aligns/KmerAlignCore.h $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/KmerTable.h $(SRC)/analysis/TranscriptomeFromVaryK.cc $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h 
analysis/TranscriptomeGraph.o: $(SRC)/aligns/KmerAlignCore.h $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/TranscriptomeGraph.cc $(SRC)/analysis/TranscriptomeGraph.h $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h 
analysis/sequenceUtil.o: $(SRC)/analysis/sequenceUtil.cc $(SRC)/analysis/sequenceUtil.h $(SRC)/analysis/stacktrace.h 
analysis/stacktrace.o: $(SRC)/analysis/stacktrace.cc $(SRC)/analysis/stacktrace.h 
base/ErrorHandling.o: $(SRC)/base/ErrorHandling.cc $(SRC)/base/ErrorHandling.h 
base/FileParser.o: $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.cc $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/util/mutil.h 
base/StringUtil.o: $(SRC)/base/StringUtil.cc $(SRC)/base/StringUtil.h 
util/mutil.o: $(SRC)/util/mutil.cc $(SRC)/util/mutil.h 
BreakTransByPairs:  checkLock
BreakTransByPairs:  aligns/KmerAlignCore.o analysis/AACodons.o analysis/BreakTransByPairs.o analysis/DNAVector.o analysis/KmerTable.o analysis/NonRedKmerTable.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
	/bin/rm -f lib_BreakTransByPairs_temp.a
	$(AR) $(ARFLAGS) lib_BreakTransByPairs_temp.a $(OBJ)/aligns/KmerAlignCore.o $(OBJ)/analysis/AACodons.o $(OBJ)/analysis/BreakTransByPairs.o $(OBJ)/analysis/DNAVector.o $(OBJ)/analysis/KmerTable.o $(OBJ)/analysis/NonRedKmerTable.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
	$(BIN)/checkLock $(BIN)/$@
	$(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@  $(OBJ)/analysis/BreakTransByPairs.o -L. $(LINK_LIBS) -l_BreakTransByPairs_temp
	/bin/rm lib_BreakTransByPairs_temp.a
Chrysalis:  checkLock
Chrysalis:  aligns/KmerAlignCore.o analysis/AACodons.o analysis/Chrysalis.o analysis/DNAVector.o analysis/TranscriptomeGraph.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
	/bin/rm -f lib_Chrysalis_temp.a
	$(AR) $(ARFLAGS) lib_Chrysalis_temp.a $(OBJ)/aligns/KmerAlignCore.o $(OBJ)/analysis/AACodons.o $(OBJ)/analysis/Chrysalis.o $(OBJ)/analysis/DNAVector.o $(OBJ)/analysis/TranscriptomeGraph.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
	$(BIN)/checkLock $(BIN)/$@
	$(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@  $(OBJ)/analysis/Chrysalis.o -L. $(LINK_LIBS) -l_Chrysalis_temp
	/bin/rm lib_Chrysalis_temp.a
GraphFromFasta:  checkLock
GraphFromFasta:  aligns/KmerAlignCore.o analysis/AACodons.o analysis/DNAVector.o analysis/DeBruijnGraph.o analysis/GraphFromFasta.o analysis/KmerTable.o analysis/NonRedKmerTable.o analysis/sequenceUtil.o analysis/stacktrace.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
	/bin/rm -f lib_GraphFromFasta_temp.a
	$(AR) $(ARFLAGS) lib_GraphFromFasta_temp.a $(OBJ)/aligns/KmerAlignCore.o $(OBJ)/analysis/AACodons.o $(OBJ)/analysis/DNAVector.o $(OBJ)/analysis/DeBruijnGraph.o $(OBJ)/analysis/GraphFromFasta.o $(OBJ)/analysis/KmerTable.o $(OBJ)/analysis/NonRedKmerTable.o $(OBJ)/analysis/sequenceUtil.o $(OBJ)/analysis/stacktrace.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
	$(BIN)/checkLock $(BIN)/$@
	$(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@  $(OBJ)/analysis/GraphFromFasta.o -L. $(LINK_LIBS) -l_GraphFromFasta_temp
	/bin/rm lib_GraphFromFasta_temp.a
IsoformAugment:  checkLock
IsoformAugment:  aligns/KmerAlignCore.o analysis/AACodons.o analysis/DNAVector.o analysis/IsoformAugment.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
	/bin/rm -f lib_IsoformAugment_temp.a
	$(AR) $(ARFLAGS) lib_IsoformAugment_temp.a $(OBJ)/aligns/KmerAlignCore.o $(OBJ)/analysis/AACodons.o $(OBJ)/analysis/DNAVector.o $(OBJ)/analysis/IsoformAugment.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
	$(BIN)/checkLock $(BIN)/$@
	$(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@  $(OBJ)/analysis/IsoformAugment.o -L. $(LINK_LIBS) -l_IsoformAugment_temp
	/bin/rm lib_IsoformAugment_temp.a
JoinTransByPairs:  checkLock
JoinTransByPairs:  aligns/KmerAlignCore.o analysis/AACodons.o analysis/DNAVector.o analysis/JoinTransByPairs.o analysis/KmerTable.o analysis/NonRedKmerTable.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
	/bin/rm -f lib_JoinTransByPairs_temp.a
	$(AR) $(ARFLAGS) lib_JoinTransByPairs_temp.a $(OBJ)/aligns/KmerAlignCore.o $(OBJ)/analysis/AACodons.o $(OBJ)/analysis/DNAVector.o $(OBJ)/analysis/JoinTransByPairs.o $(OBJ)/analysis/KmerTable.o $(OBJ)/analysis/NonRedKmerTable.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
	$(BIN)/checkLock $(BIN)/$@
	$(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@  $(OBJ)/analysis/JoinTransByPairs.o -L. $(LINK_LIBS) -l_JoinTransByPairs_temp
	/bin/rm lib_JoinTransByPairs_temp.a
QuantifyGraph:  checkLock
QuantifyGraph:  aligns/KmerAlignCore.o analysis/AACodons.o analysis/DNAVector.o analysis/KmerTable.o analysis/NonRedKmerTable.o analysis/QuantifyGraph.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
	/bin/rm -f lib_QuantifyGraph_temp.a
	$(AR) $(ARFLAGS) lib_QuantifyGraph_temp.a $(OBJ)/aligns/KmerAlignCore.o $(OBJ)/analysis/AACodons.o $(OBJ)/analysis/DNAVector.o $(OBJ)/analysis/KmerTable.o $(OBJ)/analysis/NonRedKmerTable.o $(OBJ)/analysis/QuantifyGraph.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
	$(BIN)/checkLock $(BIN)/$@
	$(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@  $(OBJ)/analysis/QuantifyGraph.o -L. $(LINK_LIBS) -l_QuantifyGraph_temp
	/bin/rm lib_QuantifyGraph_temp.a
ReadsToTranscripts:  checkLock
ReadsToTranscripts:  analysis/AACodons.o analysis/DNAVector.o analysis/NonRedKmerTable.o analysis/ReadsToTranscripts.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
	/bin/rm -f lib_ReadsToTranscripts_temp.a
	$(AR) $(ARFLAGS) lib_ReadsToTranscripts_temp.a $(OBJ)/analysis/AACodons.o $(OBJ)/analysis/DNAVector.o $(OBJ)/analysis/NonRedKmerTable.o $(OBJ)/analysis/ReadsToTranscripts.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
	$(BIN)/checkLock $(BIN)/$@
	$(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@  $(OBJ)/analysis/ReadsToTranscripts.o -L. $(LINK_LIBS) -l_ReadsToTranscripts_temp
	/bin/rm lib_ReadsToTranscripts_temp.a
RunButterfly:  checkLock
RunButterfly:  analysis/RunButterfly.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
	/bin/rm -f lib_RunButterfly_temp.a
	$(AR) $(ARFLAGS) lib_RunButterfly_temp.a $(OBJ)/analysis/RunButterfly.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
	$(BIN)/checkLock $(BIN)/$@
	$(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@  $(OBJ)/analysis/RunButterfly.o -L. $(LINK_LIBS) -l_RunButterfly_temp
	/bin/rm lib_RunButterfly_temp.a
TranscriptomeFromVaryK:  checkLock
TranscriptomeFromVaryK:  aligns/KmerAlignCore.o analysis/AACodons.o analysis/DNAVector.o analysis/KmerTable.o analysis/NonRedKmerTable.o analysis/TranscriptomeFromVaryK.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
	/bin/rm -f lib_TranscriptomeFromVaryK_temp.a
	$(AR) $(ARFLAGS) lib_TranscriptomeFromVaryK_temp.a $(OBJ)/aligns/KmerAlignCore.o $(OBJ)/analysis/AACodons.o $(OBJ)/analysis/DNAVector.o $(OBJ)/analysis/KmerTable.o $(OBJ)/analysis/NonRedKmerTable.o $(OBJ)/analysis/TranscriptomeFromVaryK.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
	$(BIN)/checkLock $(BIN)/$@
	$(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@  $(OBJ)/analysis/TranscriptomeFromVaryK.o -L. $(LINK_LIBS) -l_TranscriptomeFromVaryK_temp
	/bin/rm lib_TranscriptomeFromVaryK_temp.a

# Target lists

OBJECTS = \
  aligns/KmerAlignCore.o\
  analysis/AACodons.o\
  analysis/BreakTransByPairs.o\
  analysis/Chrysalis.o\
  analysis/DNAVector.o\
  analysis/DeBruijnGraph.o\
  analysis/GraphFromFasta.o\
  analysis/IsoformAugment.o\
  analysis/JoinTransByPairs.o\
  analysis/KmerTable.o\
  analysis/NonRedKmerTable.o\
  analysis/QuantifyGraph.o\
  analysis/ReadsToTranscripts.o\
  analysis/RunButterfly.o\
  analysis/TranscriptomeFromVaryK.o\
  analysis/TranscriptomeGraph.o\
  analysis/sequenceUtil.o\
  analysis/stacktrace.o\
  base/ErrorHandling.o\
  base/FileParser.o\
  base/StringUtil.o\
  util/mutil.o\

nolink: $(OBJECTS)

EXECUTABLES = \
  BreakTransByPairs\
  Chrysalis\
  GraphFromFasta\
  IsoformAugment\
  JoinTransByPairs\
  QuantifyGraph\
  ReadsToTranscripts\
  RunButterfly\
  TranscriptomeFromVaryK\

everything: $(EXECUTABLES)

.PHONY: analysis
analysis: \
  BreakTransByPairs\
  Chrysalis\
  GraphFromFasta\
  IsoformAugment\
  JoinTransByPairs\
  QuantifyGraph\
  ReadsToTranscripts\
  RunButterfly\
  TranscriptomeFromVaryK\

