-###################################################
-#
-# Makefile for mothur
-# Creator [Xcode -> Makefile Ver: Feb 14 2007 09:18:41]
-# Created: April 16, 2010
-#
-###################################################
-
-#
-# Macros
-#
-
-CC = g++
-CC_OPTIONS = -O3
-
-# if you do not want to use the readline library set to no, default yes.
-# make sure you have the library installed
-
-64BIT_VERSION ?= yes
-
-ifeq ($(strip $(64BIT_VERSION)),yes)
- CC_OPTIONS += -arch x86_64
- LNK_OPTIONS += -arch x86_64
-endif
-
-USEREADLINE ?= yes
-
-ifeq ($(strip $(USEREADLINE)),yes)
- CC_OPTIONS += -DUSE_READLINE
- LNK_OPTIONS += \
- -lreadline\
- -lncurses\
- -L../readline-6.0
-endif
-
-USEMPI ?= no
-
-ifeq ($(strip $(USEMPI)),yes)
- CC = mpic++
- CC_OPTIONS += -DUSE_MPI
-endif
-
-#
-# INCLUDE directories for mothur
-#
-
- INCLUDE = -I.
-
-#
-# Build mothur
-#
-
-mothur : \
- ./sharedutilities.o\
- ./treegroupscommand.o\
- ./bootstrapsharedcommand.o\
- ./matrixoutputcommand.o\
- ./getoturepcommand.o\
- ./screenseqscommand.o\
- ./chimera.o\
- ./decalc.o\
- ./readotucommand.o\
- ./readdistcommand.o\
- ./commandfactory.o\
- ./alignment.o\
- ./alignmentcell.o\
- ./gotohoverlap.o\
- ./overlap.o\
- ./needlemanoverlap.o\
- ./blastalign.o\
- ./noalign.o\
- ./suffixdb.o\
- ./suffixnodes.o\
- ./suffixtree.o\
- ./blastdb.o\
- ./nast.o\
- ./nastreport.o\
- ./boneh.o\
- ./efron.o\
- ./solow.o\
- ./unifracweightedcommand.o\
- ./weighted.o\
- ./unweighted.o\
- ./unifracunweightedcommand.o\
- ./getsabundcommand.o\
- ./getrabundcommand.o\
- ./bellerophon.o\
- ./pintail.o\
- ./sharedanderbergs.o\
- ./venncommand.o\
- ./venn.o\
- ./fullmatrix.o\
- ./heatmap.o\
- ./heatmapcommand.o\
- ./libshuffcommand.o\
- ./nocommands.o\
- ./sharedbraycurtis.o\
- ./sharedkulczynski.o\
- ./sharedlennon.o\
- ./sharedkulczynskicody.o\
- ./sharedmorisitahorn.o\
- ./sharedochiai.o\
- ./readcolumn.o\
- ./readotu.o\
- ./readphylip.o\
- ./consensuscommand.o\
- ./heatmapsimcommand.o\
- ./heatmapsim.o\
- ./optionparser.o\
- ./filterseqscommand.o\
- ./goodscoverage.o\
- ./sequencedb.o\
- ./sharedjackknife.o\
- ./sharedmarczewski.o\
- ./aligncommand.o\
- ./treemap.o\
- ./parsimonycommand.o\
- ./parsimony.o\
- ./seqsummarycommand.o\
- ./chimeraccodecommand.o\
- ./chimerabellerophoncommand.o\
- ./chimeracheckcommand.o\
- ./chimeraslayercommand.o\
- ./chimerapintailcommand.o\
- ./chimeraseqscommand.o\
- ./sharedlistvector.o\
- ./tree.o\
- ./readtree.o\
- ./sharedsobscollectsummary.o\
- ./deconvolutecommand.o\
- ./listseqscommand.o\
- ./getseqscommand.o\
- ./removeseqscommand.o\
- ./degapseqscommand.o\
- ./systemcommand.o\
- ./binsequencecommand.o\
- ./distancecommand.o\
- ./ace.o\
- ./averagelinkage.o\
- ./bootstrap.o\
- ./calculator.o\
- ./chao1.o\
- ./cluster.o\
- ./clustercommand.o\
- ./collect.o\
- ./collectcommand.o\
- ./collectsharedcommand.o\
- ./commandoptionparser.o\
- ./completelinkage.o\
- ./database.o\
- ./engine.o\
- ./fastamap.o\
- ./fileoutput.o\
- ./globaldata.o\
- ./groupmap.o\
- ./helpcommand.o\
- ./makegroupcommand.o\
- ./chopseqscommand.o\
- ./clearcutcommand.o\
- ./catchallcommand.o\
- ./splitabundcommand.o\
- ./splitmatrix.o\
- ./clustersplitcommand.o\
- ./weightedlinkage.o\
- ./inputdata.o\
- ./jackknife.o\
- ./kmer.o\
- ./kmerdb.o\
- ./listvector.o\
- ./mothur.o\
- ./nameassignment.o\
- ./npshannon.o\
- ./ordervector.o\
- ./progress.o\
- ./quitcommand.o\
- ./rabundvector.o\
- ./rarecalc.o\
- ./raredisplay.o\
- ./rarefact.o\
- ./rarefactcommand.o\
- ./rarefactsharedcommand.o\
- ./sabundvector.o\
- ./sequence.o\
- ./shannon.o\
- ./sharedace.o\
- ./sharedchao1.o\
- ./sharedcommand.o\
- ./sharedjabund.o\
- ./sharedjclass.o\
- ./sharedjest.o\
- ./sharedordervector.o\
- ./sharedrabundvector.o\
- ./sharedsabundvector.o\
- ./sharedsobs.o\
- ./sharedsorabund.o\
- ./sharedsorclass.o\
- ./sharedsorest.o\
- ./sharedthetan.o\
- ./sharedthetayc.o\
- ./simpson.o\
- ./singlelinkage.o\
- ./sparsematrix.o\
- ./summarycommand.o\
- ./summarysharedcommand.o\
- ./uvest.o\
- ./validcalculator.o\
- ./validparameter.o\
- ./treenode.o\
- ./readtreecommand.o\
- ./reversecommand.o\
- ./trimseqscommand.o\
- ./slibshuff.o\
- ./libshuff.o\
- ./dlibshuff.o\
- ./mergefilecommand.o\
- ./coverage.o\
- ./whittaker.o\
- ./preclustercommand.o\
- ./otuhierarchycommand.o\
- ./setdircommand.o\
- ./getgroupcommand.o\
- ./getlabelcommand.o\
- ./secondarystructurecommand.o\
- ./mothurout.o\
- ./parselistscommand.o\
- ./readblast.o\
- ./chimeracheckrdp.o\
- ./hclustercommand.o\
- ./hcluster.o\
- ./getlistcountcommand.o\
- ./getrelabundcommand.o\
- ./readcluster.o\
- ./ccode.o\
- ./taxonomyequalizer.o\
- ./phylotypecommand.o\
- ./classifyseqscommand.o\
- ./classifyotucommand.o\
- ./parsesffcommand.o\
- ./classify.o\
- ./phylotree.o\
- ./phylodiversity.o\
- ./phylodiversitycommand.o\
- ./bayesian.o\
- ./phylosummary.o\
- ./alignmentdb.o\
- ./knn.o\
- ./distancedb.o\
- ./chimeraslayer.o\
- ./slayer.o\
- ./pcacommand.o\
- ./formatcolumn.o\
- ./formatphylip.o\
- ./mgclustercommand.o\
- ./getsharedotucommand.o\
- ./maligner.o\
- ./chimerarealigner.o\
- ./bergerparker.o\
- ./bstick.o\
- ./sharedkstest.o\
- ./qstat.o\
- ./shen.o\
- ./logsd.o\
- ./geom.o\
- ./setlogfilecommand.o
- $(CC) $(LNK_OPTIONS) \
- ./sharedutilities.o\
- ./treegroupscommand.o\
- ./bootstrapsharedcommand.o\
- ./matrixoutputcommand.o\
- ./getoturepcommand.o\
- ./screenseqscommand.o\
- ./chimera.o\
- ./decalc.o\
- ./readotucommand.o\
- ./readdistcommand.o\
- ./commandfactory.o\
- ./alignment.o\
- ./alignmentcell.o\
- ./gotohoverlap.o\
- ./overlap.o\
- ./needlemanoverlap.o\
- ./blastalign.o\
- ./noalign.o\
- ./suffixdb.o\
- ./suffixnodes.o\
- ./suffixtree.o\
- ./blastdb.o\
- ./nast.o\
- ./nastreport.o\
- ./boneh.o\
- ./efron.o\
- ./solow.o\
- ./unifracweightedcommand.o\
- ./weighted.o\
- ./unweighted.o\
- ./unifracunweightedcommand.o\
- ./getsabundcommand.o\
- ./getrabundcommand.o\
- ./bellerophon.o\
- ./pintail.o\
- ./sharedanderbergs.o\
- ./venncommand.o\
- ./venn.o\
- ./fullmatrix.o\
- ./heatmap.o\
- ./heatmapcommand.o\
- ./libshuffcommand.o\
- ./nocommands.o\
- ./sharedbraycurtis.o\
- ./sharedkulczynski.o\
- ./sharedlennon.o\
- ./sharedkulczynskicody.o\
- ./sharedmorisitahorn.o\
- ./sharedochiai.o\
- ./readcolumn.o\
- ./readotu.o\
- ./readphylip.o\
- ./consensuscommand.o\
- ./heatmapsimcommand.o\
- ./heatmapsim.o\
- ./optionparser.o\
- ./filterseqscommand.o\
- ./goodscoverage.o\
- ./sequencedb.o\
- ./sharedjackknife.o\
- ./sharedmarczewski.o\
- ./aligncommand.o\
- ./treemap.o\
- ./parsimonycommand.o\
- ./parsimony.o\
- ./seqsummarycommand.o\
- ./chimeraccodecommand.o\
- ./chimerabellerophoncommand.o\
- ./chimeracheckcommand.o\
- ./chimeraslayercommand.o\
- ./chimerapintailcommand.o\
- ./chimeraseqscommand.o\
- ./sharedlistvector.o\
- ./tree.o\
- ./readtree.o\
- ./sharedsobscollectsummary.o\
- ./deconvolutecommand.o\
- ./listseqscommand.o\
- ./getseqscommand.o\
- ./removeseqscommand.o\
- ./degapseqscommand.o\
- ./systemcommand.o\
- ./binsequencecommand.o\
- ./distancecommand.o\
- ./ace.o\
- ./averagelinkage.o\
- ./bootstrap.o\
- ./calculator.o\
- ./chao1.o\
- ./cluster.o\
- ./clustercommand.o\
- ./collect.o\
- ./collectcommand.o\
- ./collectsharedcommand.o\
- ./commandoptionparser.o\
- ./completelinkage.o\
- ./database.o\
- ./engine.o\
- ./fastamap.o\
- ./fileoutput.o\
- ./globaldata.o\
- ./groupmap.o\
- ./helpcommand.o\
- ./makegroupcommand.o\
- ./chopseqscommand.o\
- ./clearcutcommand.o\
- ./catchallcommand.o\
- ./splitabundcommand.o\
- ./splitmatrix.o\
- ./clustersplitcommand.o\
- ./weightedlinkage.o\
- ./inputdata.o\
- ./jackknife.o\
- ./kmer.o\
- ./kmerdb.o\
- ./listvector.o\
- ./mothur.o\
- ./nameassignment.o\
- ./npshannon.o\
- ./ordervector.o\
- ./progress.o\
- ./quitcommand.o\
- ./rabundvector.o\
- ./rarecalc.o\
- ./raredisplay.o\
- ./rarefact.o\
- ./rarefactcommand.o\
- ./rarefactsharedcommand.o\
- ./sabundvector.o\
- ./sequence.o\
- ./shannon.o\
- ./sharedace.o\
- ./sharedchao1.o\
- ./sharedcommand.o\
- ./sharedjabund.o\
- ./sharedjclass.o\
- ./sharedjest.o\
- ./sharedordervector.o\
- ./sharedrabundvector.o\
- ./sharedsabundvector.o\
- ./sharedsobs.o\
- ./sharedsorabund.o\
- ./sharedsorclass.o\
- ./sharedsorest.o\
- ./sharedthetan.o\
- ./sharedthetayc.o\
- ./simpson.o\
- ./singlelinkage.o\
- ./sparsematrix.o\
- ./summarycommand.o\
- ./summarysharedcommand.o\
- ./uvest.o\
- ./validcalculator.o\
- ./validparameter.o\
- ./treenode.o\
- ./readtreecommand.o\
- ./reversecommand.o\
- ./trimseqscommand.o\
- ./slibshuff.o\
- ./libshuff.o\
- ./dlibshuff.o\
- ./mergefilecommand.o\
- ./coverage.o\
- ./whittaker.o\
- ./preclustercommand.o\
- ./otuhierarchycommand.o\
- ./setdircommand.o\
- ./getgroupcommand.o\
- ./getlabelcommand.o\
- ./secondarystructurecommand.o\
- ./mothurout.o\
- ./parselistscommand.o\
- ./readblast.o\
- ./chimeracheckrdp.o\
- ./hclustercommand.o\
- ./hcluster.o\
- ./getlistcountcommand.o\
- ./getrelabundcommand.o\
- ./readcluster.o\
- ./ccode.o\
- ./taxonomyequalizer.o\
- ./phylotypecommand.o\
- ./classifyseqscommand.o\
- ./classifyotucommand.o\
- ./parsesffcommand.o\
- ./classify.o\
- ./phylotree.o\
- ./phylodiversity.o\
- ./phylodiversitycommand.o\
- ./bayesian.o\
- ./phylosummary.o\
- ./alignmentdb.o\
- ./knn.o\
- ./distancedb.o\
- ./chimeraslayer.o\
- ./slayer.o\
- ./pcacommand.o\
- ./formatcolumn.o\
- ./formatphylip.o\
- ./mgclustercommand.o\
- ./getsharedotucommand.o\
- ./maligner.o\
- ./chimerarealigner.o\
- ./bergerparker.o\
- ./bstick.o\
- ./sharedkstest.o\
- ./qstat.o\
- ./shen.o\
- ./logsd.o\
- ./geom.o\
- ./setlogfilecommand.o\
- -o ../Release/mothur
-
-clean :
- rm \
- ./sharedutilities.o\
- ./treegroupscommand.o\
- ./bootstrapsharedcommand.o\
- ./matrixoutputcommand.o\
- ./getoturepcommand.o\
- ./screenseqscommand.o\
- ./chimera.o\
- ./decalc.o\
- ./readotucommand.o\
- ./readdistcommand.o\
- ./commandfactory.o\
- ./alignment.o\
- ./alignmentcell.o\
- ./gotohoverlap.o\
- ./overlap.o\
- ./needlemanoverlap.o\
- ./blastalign.o\
- ./noalign.o\
- ./suffixdb.o\
- ./suffixnodes.o\
- ./suffixtree.o\
- ./blastdb.o\
- ./nast.o\
- ./nastreport.o\
- ./boneh.o\
- ./efron.o\
- ./solow.o\
- ./unifracweightedcommand.o\
- ./weighted.o\
- ./unweighted.o\
- ./unifracunweightedcommand.o\
- ./getsabundcommand.o\
- ./getrabundcommand.o\
- ./bellerophon.o\
- ./pintail.o\
- ./sharedanderbergs.o\
- ./venncommand.o\
- ./venn.o\
- ./fullmatrix.o\
- ./heatmap.o\
- ./heatmapcommand.o\
- ./libshuffcommand.o\
- ./nocommands.o\
- ./sharedbraycurtis.o\
- ./sharedkulczynski.o\
- ./sharedlennon.o\
- ./sharedkulczynskicody.o\
- ./sharedmorisitahorn.o\
- ./sharedochiai.o\
- ./readcolumn.o\
- ./readotu.o\
- ./readphylip.o\
- ./consensuscommand.o\
- ./heatmapsimcommand.o\
- ./heatmapsim.o\
- ./optionparser.o\
- ./filterseqscommand.o\
- ./goodscoverage.o\
- ./sequencedb.o\
- ./sharedjackknife.o\
- ./sharedmarczewski.o\
- ./aligncommand.o\
- ./treemap.o\
- ./parsimonycommand.o\
- ./parsimony.o\
- ./seqsummarycommand.o\
- ./chimeraccodecommand.o\
- ./chimerabellerophoncommand.o\
- ./chimeracheckcommand.o\
- ./chimeraslayercommand.o\
- ./chimerapintailcommand.o\
- ./chimeraseqscommand.o\
- ./sharedlistvector.o\
- ./tree.o\
- ./readtree.o\
- ./sharedsobscollectsummary.o\
- ./deconvolutecommand.o\
- ./listseqscommand.o\
- ./getseqscommand.o\
- ./removeseqscommand.o\
- ./degapseqscommand.o\
- ./systemcommand.o\
- ./binsequencecommand.o\
- ./distancecommand.o\
- ./ace.o\
- ./averagelinkage.o\
- ./bootstrap.o\
- ./calculator.o\
- ./chao1.o\
- ./cluster.o\
- ./clustercommand.o\
- ./collect.o\
- ./collectcommand.o\
- ./collectsharedcommand.o\
- ./commandoptionparser.o\
- ./completelinkage.o\
- ./database.o\
- ./engine.o\
- ./fastamap.o\
- ./fileoutput.o\
- ./globaldata.o\
- ./groupmap.o\
- ./helpcommand.o\
- ./makegroupcommand.o\
- ./chopseqscommand.o\
- ./clearcutcommand.o\
- ./catchallcommand.o\
- ./splitabundcommand.o\
- ./splitmatrix.o\
- ./clustersplitcommand.o\
- ./weightedlinkage.o\
- ./inputdata.o\
- ./jackknife.o\
- ./kmer.o\
- ./kmerdb.o\
- ./listvector.o\
- ./mothur.o\
- ./nameassignment.o\
- ./npshannon.o\
- ./ordervector.o\
- ./progress.o\
- ./quitcommand.o\
- ./rabundvector.o\
- ./rarecalc.o\
- ./raredisplay.o\
- ./rarefact.o\
- ./rarefactcommand.o\
- ./rarefactsharedcommand.o\
- ./sabundvector.o\
- ./sequence.o\
- ./shannon.o\
- ./sharedace.o\
- ./sharedchao1.o\
- ./sharedcommand.o\
- ./sharedjabund.o\
- ./sharedjclass.o\
- ./sharedjest.o\
- ./sharedordervector.o\
- ./sharedrabundvector.o\
- ./sharedsabundvector.o\
- ./sharedsobs.o\
- ./sharedsorabund.o\
- ./sharedsorclass.o\
- ./sharedsorest.o\
- ./sharedthetan.o\
- ./sharedthetayc.o\
- ./simpson.o\
- ./singlelinkage.o\
- ./sparsematrix.o\
- ./summarycommand.o\
- ./summarysharedcommand.o\
- ./uvest.o\
- ./validcalculator.o\
- ./validparameter.o\
- ./treenode.o\
- ./readtreecommand.o\
- ./reversecommand.o\
- ./trimseqscommand.o\
- ./slibshuff.o\
- ./libshuff.o\
- ./dlibshuff.o\
- ./mergefilecommand.o\
- ./coverage.o\
- ./whittaker.o\
- ./preclustercommand.o\
- ./otuhierarchycommand.o\
- ./setdircommand.o\
- ./getgroupcommand.o\
- ./getlabelcommand.o\
- ./secondarystructurecommand.o\
- ./mothurout.o\
- ./parselistscommand.o\
- ./readblast.o\
- ./chimeracheckrdp.o\
- ./hclustercommand.o\
- ./hcluster.o\
- ./getlistcountcommand.o\
- ./getrelabundcommand.o\
- ./readcluster.o\
- ./ccode.o\
- ./taxonomyequalizer.o\
- ./phylotypecommand.o\
- ./classifyseqscommand.o\
- ./classifyotucommand.o\
- ./parsesffcommand.o\
- ./classify.o\
- ./phylotree.o\
- ./phylodiversity.o\
- ./phylodiversitycommand.o\
- ./bayesian.o\
- ./phylosummary.o\
- ./alignmentdb.o\
- ./knn.o\
- ./distancedb.o\
- ./chimeraslayer.o\
- ./slayer.o\
- ./pcacommand.o\
- ./formatcolumn.o\
- ./formatphylip.o\
- ./mgclustercommand.o\
- ./getsharedotucommand.o\
- ./maligner.o\
- ./chimerarealigner.o\
- ./bergerparker.o\
- ./bstick.o\
- ./sharedkstest.o\
- ./qstat.o\
- ./shen.o\
- ./logsd.o\
- ./geom.o\
- ./setlogfilecommand.o\
- mothur
-
-install : mothur
- #cp mothur ../Release/mothur
-
-#
-# Build the parts of mothur
-#
-
-
-# Item # 1 -- sharedutilities --
-./sharedutilities.o : sharedutilities.cpp
- $(CC) $(CC_OPTIONS) sharedutilities.cpp -c $(INCLUDE) -o ./sharedutilities.o
-
-
-# Item # 2 -- treegroupscommand --
-./treegroupscommand.o : treegroupscommand.cpp
- $(CC) $(CC_OPTIONS) treegroupscommand.cpp -c $(INCLUDE) -o ./treegroupscommand.o
-
-
-# Item # 3 -- bootstrapsharedcommand --
-./bootstrapsharedcommand.o : bootstrapsharedcommand.cpp
- $(CC) $(CC_OPTIONS) bootstrapsharedcommand.cpp -c $(INCLUDE) -o ./bootstrapsharedcommand.o
-
-
-# Item # 4 -- matrixoutputcommand --
-./matrixoutputcommand.o : matrixoutputcommand.cpp
- $(CC) $(CC_OPTIONS) matrixoutputcommand.cpp -c $(INCLUDE) -o ./matrixoutputcommand.o
-
-
-# Item # 5 -- getoturepcommand --
-./getoturepcommand.o : getoturepcommand.cpp
- $(CC) $(CC_OPTIONS) getoturepcommand.cpp -c $(INCLUDE) -o ./getoturepcommand.o
-
-
-# Item # 6 -- screenseqscommand --
-./screenseqscommand.o : screenseqscommand.cpp
- $(CC) $(CC_OPTIONS) screenseqscommand.cpp -c $(INCLUDE) -o ./screenseqscommand.o
-
-
-# Item # 7 -- chimera --
-./chimera.o : chimera.cpp
- $(CC) $(CC_OPTIONS) chimera.cpp -c $(INCLUDE) -o ./chimera.o
-
-
-# Item # 8 -- decalc --
-./decalc.o : decalc.cpp
- $(CC) $(CC_OPTIONS) decalc.cpp -c $(INCLUDE) -o ./decalc.o
-
-
-# Item # 9 -- readotucommand --
-./readotucommand.o : readotucommand.cpp
- $(CC) $(CC_OPTIONS) readotucommand.cpp -c $(INCLUDE) -o ./readotucommand.o
-
-
-# Item # 10 -- readdistcommand --
-./readdistcommand.o : readdistcommand.cpp
- $(CC) $(CC_OPTIONS) readdistcommand.cpp -c $(INCLUDE) -o ./readdistcommand.o
-
-
-# Item # 11 -- commandfactory --
-./commandfactory.o : commandfactory.cpp
- $(CC) $(CC_OPTIONS) commandfactory.cpp -c $(INCLUDE) -o ./commandfactory.o
-
-
-# Item # 12 -- alignment --
-./alignment.o : alignment.cpp
- $(CC) $(CC_OPTIONS) alignment.cpp -c $(INCLUDE) -o ./alignment.o
-
-
-# Item # 13 -- alignmentcell --
-./alignmentcell.o : alignmentcell.cpp
- $(CC) $(CC_OPTIONS) alignmentcell.cpp -c $(INCLUDE) -o ./alignmentcell.o
-
-
-# Item # 14 -- gotohoverlap --
-./gotohoverlap.o : gotohoverlap.cpp
- $(CC) $(CC_OPTIONS) gotohoverlap.cpp -c $(INCLUDE) -o ./gotohoverlap.o
-
-
-# Item # 15 -- overlap --
-./overlap.o : overlap.cpp
- $(CC) $(CC_OPTIONS) overlap.cpp -c $(INCLUDE) -o ./overlap.o
-
-
-# Item # 16 -- needlemanoverlap --
-./needlemanoverlap.o : needlemanoverlap.cpp
- $(CC) $(CC_OPTIONS) needlemanoverlap.cpp -c $(INCLUDE) -o ./needlemanoverlap.o
-
-
-# Item # 17 -- blastalign --
-./blastalign.o : blastalign.cpp
- $(CC) $(CC_OPTIONS) blastalign.cpp -c $(INCLUDE) -o ./blastalign.o
-
-
-# Item # 18 -- noalign --
-./noalign.o : noalign.cpp
- $(CC) $(CC_OPTIONS) noalign.cpp -c $(INCLUDE) -o ./noalign.o
-
-
-# Item # 19 -- suffixdb --
-./suffixdb.o : suffixdb.cpp
- $(CC) $(CC_OPTIONS) suffixdb.cpp -c $(INCLUDE) -o ./suffixdb.o
-
-
-# Item # 20 -- suffixnodes --
-./suffixnodes.o : suffixnodes.cpp
- $(CC) $(CC_OPTIONS) suffixnodes.cpp -c $(INCLUDE) -o ./suffixnodes.o
-
-
-# Item # 21 -- suffixtree --
-./suffixtree.o : suffixtree.cpp
- $(CC) $(CC_OPTIONS) suffixtree.cpp -c $(INCLUDE) -o ./suffixtree.o
-
-
-# Item # 22 -- blastdb --
-./blastdb.o : blastdb.cpp
- $(CC) $(CC_OPTIONS) blastdb.cpp -c $(INCLUDE) -o ./blastdb.o
-
-
-# Item # 23 -- nast --
-./nast.o : nast.cpp
- $(CC) $(CC_OPTIONS) nast.cpp -c $(INCLUDE) -o ./nast.o
-
-
-# Item # 24 -- nastreport --
-./nastreport.o : nastreport.cpp
- $(CC) $(CC_OPTIONS) nastreport.cpp -c $(INCLUDE) -o ./nastreport.o
-
-
-# Item # 25 -- boneh --
-./boneh.o : boneh.cpp
- $(CC) $(CC_OPTIONS) boneh.cpp -c $(INCLUDE) -o ./boneh.o
-
-
-# Item # 26 -- efron --
-./efron.o : efron.cpp
- $(CC) $(CC_OPTIONS) efron.cpp -c $(INCLUDE) -o ./efron.o
-
-
-# Item # 27 -- solow --
-./solow.o : solow.cpp
- $(CC) $(CC_OPTIONS) solow.cpp -c $(INCLUDE) -o ./solow.o
-
-
-# Item # 28 -- unifracweightedcommand --
-./unifracweightedcommand.o : unifracweightedcommand.cpp
- $(CC) $(CC_OPTIONS) unifracweightedcommand.cpp -c $(INCLUDE) -o ./unifracweightedcommand.o
-
-
-# Item # 29 -- weighted --
-./weighted.o : weighted.cpp
- $(CC) $(CC_OPTIONS) weighted.cpp -c $(INCLUDE) -o ./weighted.o
-
-
-# Item # 30 -- unweighted --
-./unweighted.o : unweighted.cpp
- $(CC) $(CC_OPTIONS) unweighted.cpp -c $(INCLUDE) -o ./unweighted.o
-
-
-# Item # 31 -- unifracunweightedcommand --
-./unifracunweightedcommand.o : unifracunweightedcommand.cpp
- $(CC) $(CC_OPTIONS) unifracunweightedcommand.cpp -c $(INCLUDE) -o ./unifracunweightedcommand.o
-
-
-# Item # 32 -- getsabundcommand --
-./getsabundcommand.o : getsabundcommand.cpp
- $(CC) $(CC_OPTIONS) getsabundcommand.cpp -c $(INCLUDE) -o ./getsabundcommand.o
-
-
-# Item # 33 -- getrabundcommand --
-./getrabundcommand.o : getrabundcommand.cpp
- $(CC) $(CC_OPTIONS) getrabundcommand.cpp -c $(INCLUDE) -o ./getrabundcommand.o
-
-
-# Item # 34 -- bellerophon --
-./bellerophon.o : bellerophon.cpp
- $(CC) $(CC_OPTIONS) bellerophon.cpp -c $(INCLUDE) -o ./bellerophon.o
-
-
-# Item # 35 -- pintail --
-./pintail.o : pintail.cpp
- $(CC) $(CC_OPTIONS) pintail.cpp -c $(INCLUDE) -o ./pintail.o
-
-
-# Item # 36 -- sharedanderbergs --
-./sharedanderbergs.o : sharedanderbergs.cpp
- $(CC) $(CC_OPTIONS) sharedanderbergs.cpp -c $(INCLUDE) -o ./sharedanderbergs.o
-
-
-# Item # 37 -- venncommand --
-./venncommand.o : venncommand.cpp
- $(CC) $(CC_OPTIONS) venncommand.cpp -c $(INCLUDE) -o ./venncommand.o
-
-
-# Item # 38 -- venn --
-./venn.o : venn.cpp
- $(CC) $(CC_OPTIONS) venn.cpp -c $(INCLUDE) -o ./venn.o
-
-
-# Item # 39 -- fullmatrix --
-./fullmatrix.o : fullmatrix.cpp
- $(CC) $(CC_OPTIONS) fullmatrix.cpp -c $(INCLUDE) -o ./fullmatrix.o
-
-
-# Item # 40 -- heatmap --
-./heatmap.o : heatmap.cpp
- $(CC) $(CC_OPTIONS) heatmap.cpp -c $(INCLUDE) -o ./heatmap.o
-
-
-# Item # 41 -- heatmapcommand --
-./heatmapcommand.o : heatmapcommand.cpp
- $(CC) $(CC_OPTIONS) heatmapcommand.cpp -c $(INCLUDE) -o ./heatmapcommand.o
-
-
-# Item # 42 -- libshuffcommand --
-./libshuffcommand.o : libshuffcommand.cpp
- $(CC) $(CC_OPTIONS) libshuffcommand.cpp -c $(INCLUDE) -o ./libshuffcommand.o
-
-
-# Item # 43 -- nocommands --
-./nocommands.o : nocommands.cpp
- $(CC) $(CC_OPTIONS) nocommands.cpp -c $(INCLUDE) -o ./nocommands.o
-
-
-# Item # 44 -- sharedbraycurtis --
-./sharedbraycurtis.o : sharedbraycurtis.cpp
- $(CC) $(CC_OPTIONS) sharedbraycurtis.cpp -c $(INCLUDE) -o ./sharedbraycurtis.o
-
-
-# Item # 45 -- sharedkulczynski --
-./sharedkulczynski.o : sharedkulczynski.cpp
- $(CC) $(CC_OPTIONS) sharedkulczynski.cpp -c $(INCLUDE) -o ./sharedkulczynski.o
-
-
-# Item # 46 -- sharedlennon --
-./sharedlennon.o : sharedlennon.cpp
- $(CC) $(CC_OPTIONS) sharedlennon.cpp -c $(INCLUDE) -o ./sharedlennon.o
-
-
-# Item # 47 -- sharedkulczynskicody --
-./sharedkulczynskicody.o : sharedkulczynskicody.cpp
- $(CC) $(CC_OPTIONS) sharedkulczynskicody.cpp -c $(INCLUDE) -o ./sharedkulczynskicody.o
-
-
-# Item # 48 -- sharedmorisitahorn --
-./sharedmorisitahorn.o : sharedmorisitahorn.cpp
- $(CC) $(CC_OPTIONS) sharedmorisitahorn.cpp -c $(INCLUDE) -o ./sharedmorisitahorn.o
-
-
-# Item # 49 -- sharedochiai --
-./sharedochiai.o : sharedochiai.cpp
- $(CC) $(CC_OPTIONS) sharedochiai.cpp -c $(INCLUDE) -o ./sharedochiai.o
-
-
-# Item # 50 -- readcolumn --
-./readcolumn.o : readcolumn.cpp
- $(CC) $(CC_OPTIONS) readcolumn.cpp -c $(INCLUDE) -o ./readcolumn.o
-
-
-# Item # 51 -- readotu --
-./readotu.o : readotu.cpp
- $(CC) $(CC_OPTIONS) readotu.cpp -c $(INCLUDE) -o ./readotu.o
-
-
-# Item # 52 -- readphylip --
-./readphylip.o : readphylip.cpp
- $(CC) $(CC_OPTIONS) readphylip.cpp -c $(INCLUDE) -o ./readphylip.o
-
-
-# Item # 53 -- consensuscommand --
-./consensuscommand.o : consensuscommand.cpp
- $(CC) $(CC_OPTIONS) consensuscommand.cpp -c $(INCLUDE) -o ./consensuscommand.o
-
-
-# Item # 54 -- heatmapsimcommand --
-./heatmapsimcommand.o : heatmapsimcommand.cpp
- $(CC) $(CC_OPTIONS) heatmapsimcommand.cpp -c $(INCLUDE) -o ./heatmapsimcommand.o
-
-
-# Item # 55 -- heatmapsim --
-./heatmapsim.o : heatmapsim.cpp
- $(CC) $(CC_OPTIONS) heatmapsim.cpp -c $(INCLUDE) -o ./heatmapsim.o
-
-
-# Item # 56 -- optionparser --
-./optionparser.o : optionparser.cpp
- $(CC) $(CC_OPTIONS) optionparser.cpp -c $(INCLUDE) -o ./optionparser.o
-
-
-# Item # 57 -- filterseqscommand --
-./filterseqscommand.o : filterseqscommand.cpp
- $(CC) $(CC_OPTIONS) filterseqscommand.cpp -c $(INCLUDE) -o ./filterseqscommand.o
-
-
-# Item # 58 -- goodscoverage --
-./goodscoverage.o : goodscoverage.cpp
- $(CC) $(CC_OPTIONS) goodscoverage.cpp -c $(INCLUDE) -o ./goodscoverage.o
-
-
-# Item # 59 -- sequencedb --
-./sequencedb.o : sequencedb.cpp
- $(CC) $(CC_OPTIONS) sequencedb.cpp -c $(INCLUDE) -o ./sequencedb.o
-
-
-# Item # 60 -- sharedjackknife --
-./sharedjackknife.o : sharedjackknife.cpp
- $(CC) $(CC_OPTIONS) sharedjackknife.cpp -c $(INCLUDE) -o ./sharedjackknife.o
-
-
-# Item # 61 -- sharedmarczewski --
-./sharedmarczewski.o : sharedmarczewski.cpp
- $(CC) $(CC_OPTIONS) sharedmarczewski.cpp -c $(INCLUDE) -o ./sharedmarczewski.o
-
-
-# Item # 62 -- aligncommand --
-./aligncommand.o : aligncommand.cpp
- $(CC) $(CC_OPTIONS) aligncommand.cpp -c $(INCLUDE) -o ./aligncommand.o
-
-
-# Item # 63 -- treemap --
-./treemap.o : treemap.cpp
- $(CC) $(CC_OPTIONS) treemap.cpp -c $(INCLUDE) -o ./treemap.o
-
-
-# Item # 64 -- parsimonycommand --
-./parsimonycommand.o : parsimonycommand.cpp
- $(CC) $(CC_OPTIONS) parsimonycommand.cpp -c $(INCLUDE) -o ./parsimonycommand.o
-
-
-# Item # 65 -- parsimony --
-./parsimony.o : parsimony.cpp
- $(CC) $(CC_OPTIONS) parsimony.cpp -c $(INCLUDE) -o ./parsimony.o
-
-
-# Item # 66 -- seqsummarycommand --
-./seqsummarycommand.o : seqsummarycommand.cpp
- $(CC) $(CC_OPTIONS) seqsummarycommand.cpp -c $(INCLUDE) -o ./seqsummarycommand.o
-
-
-# Item # 67 -- chimeraseqscommand --
-./chimeraseqscommand.o : chimeraseqscommand.cpp
- $(CC) $(CC_OPTIONS) chimeraseqscommand.cpp -c $(INCLUDE) -o ./chimeraseqscommand.o
-
-
-# Item # 68 -- sharedlistvector --
-./sharedlistvector.o : sharedlistvector.cpp
- $(CC) $(CC_OPTIONS) sharedlistvector.cpp -c $(INCLUDE) -o ./sharedlistvector.o
-
-
-# Item # 69 -- tree --
-./tree.o : tree.cpp
- $(CC) $(CC_OPTIONS) tree.cpp -c $(INCLUDE) -o ./tree.o
-
-
-# Item # 70 -- readtree --
-./readtree.o : readtree.cpp
- $(CC) $(CC_OPTIONS) readtree.cpp -c $(INCLUDE) -o ./readtree.o
-
-
-# Item # 71 -- sharedsobscollectsummary --
-./sharedsobscollectsummary.o : sharedsobscollectsummary.cpp
- $(CC) $(CC_OPTIONS) sharedsobscollectsummary.cpp -c $(INCLUDE) -o ./sharedsobscollectsummary.o
-
-
-# Item # 72 -- deconvolutecommand --
-./deconvolutecommand.o : deconvolutecommand.cpp
- $(CC) $(CC_OPTIONS) deconvolutecommand.cpp -c $(INCLUDE) -o ./deconvolutecommand.o
-
-
-# Item # 73 -- listseqscommand --
-./listseqscommand.o : listseqscommand.cpp
- $(CC) $(CC_OPTIONS) listseqscommand.cpp -c $(INCLUDE) -o ./listseqscommand.o
-
-
-# Item # 74 -- getseqscommand --
-./getseqscommand.o : getseqscommand.cpp
- $(CC) $(CC_OPTIONS) getseqscommand.cpp -c $(INCLUDE) -o ./getseqscommand.o
-
-
-# Item # 75 -- removeseqscommand --
-./removeseqscommand.o : removeseqscommand.cpp
- $(CC) $(CC_OPTIONS) removeseqscommand.cpp -c $(INCLUDE) -o ./removeseqscommand.o
-
-
-# Item # 76 -- systemcommand --
-./systemcommand.o : systemcommand.cpp
- $(CC) $(CC_OPTIONS) systemcommand.cpp -c $(INCLUDE) -o ./systemcommand.o
-
-
-# Item # 77 -- binsequencecommand --
-./binsequencecommand.o : binsequencecommand.cpp
- $(CC) $(CC_OPTIONS) binsequencecommand.cpp -c $(INCLUDE) -o ./binsequencecommand.o
-
-
-# Item # 78 -- distancecommand --
-./distancecommand.o : distancecommand.cpp
- $(CC) $(CC_OPTIONS) distancecommand.cpp -c $(INCLUDE) -o ./distancecommand.o
-
-
-# Item # 79 -- ace --
-./ace.o : ace.cpp
- $(CC) $(CC_OPTIONS) ace.cpp -c $(INCLUDE) -o ./ace.o
-
-
-# Item # 80 -- averagelinkage --
-./averagelinkage.o : averagelinkage.cpp
- $(CC) $(CC_OPTIONS) averagelinkage.cpp -c $(INCLUDE) -o ./averagelinkage.o
-
-
-# Item # 81 -- bootstrap --
-./bootstrap.o : bootstrap.cpp
- $(CC) $(CC_OPTIONS) bootstrap.cpp -c $(INCLUDE) -o ./bootstrap.o
-
-
-# Item # 82 -- calculator --
-./calculator.o : calculator.cpp
- $(CC) $(CC_OPTIONS) calculator.cpp -c $(INCLUDE) -o ./calculator.o
-
-
-# Item # 83 -- chao1 --
-./chao1.o : chao1.cpp
- $(CC) $(CC_OPTIONS) chao1.cpp -c $(INCLUDE) -o ./chao1.o
-
-
-# Item # 84 -- cluster --
-./cluster.o : cluster.cpp
- $(CC) $(CC_OPTIONS) cluster.cpp -c $(INCLUDE) -o ./cluster.o
-
-
-# Item # 85 -- clustercommand --
-./clustercommand.o : clustercommand.cpp
- $(CC) $(CC_OPTIONS) clustercommand.cpp -c $(INCLUDE) -o ./clustercommand.o
-
-
-# Item # 86 -- collect --
-./collect.o : collect.cpp
- $(CC) $(CC_OPTIONS) collect.cpp -c $(INCLUDE) -o ./collect.o
-
-
-# Item # 87 -- collectcommand --
-./collectcommand.o : collectcommand.cpp
- $(CC) $(CC_OPTIONS) collectcommand.cpp -c $(INCLUDE) -o ./collectcommand.o
-
-
-# Item # 88 -- collectsharedcommand --
-./collectsharedcommand.o : collectsharedcommand.cpp
- $(CC) $(CC_OPTIONS) collectsharedcommand.cpp -c $(INCLUDE) -o ./collectsharedcommand.o
-
-
-# Item # 89 -- commandoptionparser --
-./commandoptionparser.o : commandoptionparser.cpp
- $(CC) $(CC_OPTIONS) commandoptionparser.cpp -c $(INCLUDE) -o ./commandoptionparser.o
-
-
-# Item # 90 -- completelinkage --
-./completelinkage.o : completelinkage.cpp
- $(CC) $(CC_OPTIONS) completelinkage.cpp -c $(INCLUDE) -o ./completelinkage.o
-
-
-# Item # 91 -- database --
-./database.o : database.cpp
- $(CC) $(CC_OPTIONS) database.cpp -c $(INCLUDE) -o ./database.o
-
-
-# Item # 92 -- engine --
-./engine.o : engine.cpp
- $(CC) $(CC_OPTIONS) engine.cpp -c $(INCLUDE) -o ./engine.o
-
-
-# Item # 93 -- fastamap --
-./fastamap.o : fastamap.cpp
- $(CC) $(CC_OPTIONS) fastamap.cpp -c $(INCLUDE) -o ./fastamap.o
-
-
-# Item # 94 -- fileoutput --
-./fileoutput.o : fileoutput.cpp
- $(CC) $(CC_OPTIONS) fileoutput.cpp -c $(INCLUDE) -o ./fileoutput.o
-
-
-# Item # 95 -- globaldata --
-./globaldata.o : globaldata.cpp
- $(CC) $(CC_OPTIONS) globaldata.cpp -c $(INCLUDE) -o ./globaldata.o
-
-
-# Item # 96 -- groupmap --
-./groupmap.o : groupmap.cpp
- $(CC) $(CC_OPTIONS) groupmap.cpp -c $(INCLUDE) -o ./groupmap.o
-
-
-# Item # 97 -- helpcommand --
-./helpcommand.o : helpcommand.cpp
- $(CC) $(CC_OPTIONS) helpcommand.cpp -c $(INCLUDE) -o ./helpcommand.o
-
-
-# Item # 98 -- inputdata --
-./inputdata.o : inputdata.cpp
- $(CC) $(CC_OPTIONS) inputdata.cpp -c $(INCLUDE) -o ./inputdata.o
-
-
-# Item # 99 -- jackknife --
-./jackknife.o : jackknife.cpp
- $(CC) $(CC_OPTIONS) jackknife.cpp -c $(INCLUDE) -o ./jackknife.o
-
-
-# Item # 100 -- kmer --
-./kmer.o : kmer.cpp
- $(CC) $(CC_OPTIONS) kmer.cpp -c $(INCLUDE) -o ./kmer.o
-
-
-# Item # 101 -- kmerdb --
-./kmerdb.o : kmerdb.cpp
- $(CC) $(CC_OPTIONS) kmerdb.cpp -c $(INCLUDE) -o ./kmerdb.o
-
-
-# Item # 102 -- listvector --
-./listvector.o : listvector.cpp
- $(CC) $(CC_OPTIONS) listvector.cpp -c $(INCLUDE) -o ./listvector.o
-
-
-# Item # 103 -- mothur --
-./mothur.o : mothur.cpp
- $(CC) $(CC_OPTIONS) mothur.cpp -c $(INCLUDE) -o ./mothur.o
-
-
-# Item # 104 -- nameassignment --
-./nameassignment.o : nameassignment.cpp
- $(CC) $(CC_OPTIONS) nameassignment.cpp -c $(INCLUDE) -o ./nameassignment.o
-
-
-# Item # 105 -- npshannon --
-./npshannon.o : npshannon.cpp
- $(CC) $(CC_OPTIONS) npshannon.cpp -c $(INCLUDE) -o ./npshannon.o
-
-
-# Item # 106 -- ordervector --
-./ordervector.o : ordervector.cpp
- $(CC) $(CC_OPTIONS) ordervector.cpp -c $(INCLUDE) -o ./ordervector.o
-
-
-# Item # 107 -- progress --
-./progress.o : progress.cpp
- $(CC) $(CC_OPTIONS) progress.cpp -c $(INCLUDE) -o ./progress.o
-
-
-# Item # 108 -- quitcommand --
-./quitcommand.o : quitcommand.cpp
- $(CC) $(CC_OPTIONS) quitcommand.cpp -c $(INCLUDE) -o ./quitcommand.o
-
-
-# Item # 109 -- rabundvector --
-./rabundvector.o : rabundvector.cpp
- $(CC) $(CC_OPTIONS) rabundvector.cpp -c $(INCLUDE) -o ./rabundvector.o
-
-
-# Item # 110 -- rarecalc --
-./rarecalc.o : rarecalc.cpp
- $(CC) $(CC_OPTIONS) rarecalc.cpp -c $(INCLUDE) -o ./rarecalc.o
-
-
-# Item # 111 -- raredisplay --
-./raredisplay.o : raredisplay.cpp
- $(CC) $(CC_OPTIONS) raredisplay.cpp -c $(INCLUDE) -o ./raredisplay.o
-
-
-# Item # 112 -- rarefact --
-./rarefact.o : rarefact.cpp
- $(CC) $(CC_OPTIONS) rarefact.cpp -c $(INCLUDE) -o ./rarefact.o
-
-
-# Item # 113 -- rarefactcommand --
-./rarefactcommand.o : rarefactcommand.cpp
- $(CC) $(CC_OPTIONS) rarefactcommand.cpp -c $(INCLUDE) -o ./rarefactcommand.o
-
-
-# Item # 114 -- rarefactsharedcommand --
-./rarefactsharedcommand.o : rarefactsharedcommand.cpp
- $(CC) $(CC_OPTIONS) rarefactsharedcommand.cpp -c $(INCLUDE) -o ./rarefactsharedcommand.o
-
-
-# Item # 115 -- sabundvector --
-./sabundvector.o : sabundvector.cpp
- $(CC) $(CC_OPTIONS) sabundvector.cpp -c $(INCLUDE) -o ./sabundvector.o
-
-
-# Item # 116 -- sequence --
-./sequence.o : sequence.cpp
- $(CC) $(CC_OPTIONS) sequence.cpp -c $(INCLUDE) -o ./sequence.o
-
-
-# Item # 117 -- shannon --
-./shannon.o : shannon.cpp
- $(CC) $(CC_OPTIONS) shannon.cpp -c $(INCLUDE) -o ./shannon.o
-
-
-# Item # 118 -- sharedace --
-./sharedace.o : sharedace.cpp
- $(CC) $(CC_OPTIONS) sharedace.cpp -c $(INCLUDE) -o ./sharedace.o
-
-
-# Item # 119 -- sharedchao1 --
-./sharedchao1.o : sharedchao1.cpp
- $(CC) $(CC_OPTIONS) sharedchao1.cpp -c $(INCLUDE) -o ./sharedchao1.o
-
-
-# Item # 120 -- sharedcommand --
-./sharedcommand.o : sharedcommand.cpp
- $(CC) $(CC_OPTIONS) sharedcommand.cpp -c $(INCLUDE) -o ./sharedcommand.o
-
-
-# Item # 121 -- sharedjabund --
-./sharedjabund.o : sharedjabund.cpp
- $(CC) $(CC_OPTIONS) sharedjabund.cpp -c $(INCLUDE) -o ./sharedjabund.o
-
-
-# Item # 122 -- sharedjclass --
-./sharedjclass.o : sharedjclass.cpp
- $(CC) $(CC_OPTIONS) sharedjclass.cpp -c $(INCLUDE) -o ./sharedjclass.o
-
-
-# Item # 123 -- sharedjest --
-./sharedjest.o : sharedjest.cpp
- $(CC) $(CC_OPTIONS) sharedjest.cpp -c $(INCLUDE) -o ./sharedjest.o
-
-
-# Item # 124 -- sharedordervector --
-./sharedordervector.o : sharedordervector.cpp
- $(CC) $(CC_OPTIONS) sharedordervector.cpp -c $(INCLUDE) -o ./sharedordervector.o
-
-
-# Item # 125 -- sharedrabundvector --
-./sharedrabundvector.o : sharedrabundvector.cpp
- $(CC) $(CC_OPTIONS) sharedrabundvector.cpp -c $(INCLUDE) -o ./sharedrabundvector.o
-
-
-# Item # 126 -- sharedsabundvector --
-./sharedsabundvector.o : sharedsabundvector.cpp
- $(CC) $(CC_OPTIONS) sharedsabundvector.cpp -c $(INCLUDE) -o ./sharedsabundvector.o
-
-
-# Item # 127 -- sharedsobs --
-./sharedsobs.o : sharedsobs.cpp
- $(CC) $(CC_OPTIONS) sharedsobs.cpp -c $(INCLUDE) -o ./sharedsobs.o
-
-
-# Item # 128 -- sharedsorabund --
-./sharedsorabund.o : sharedsorabund.cpp
- $(CC) $(CC_OPTIONS) sharedsorabund.cpp -c $(INCLUDE) -o ./sharedsorabund.o
-
-
-# Item # 129 -- sharedsorclass --
-./sharedsorclass.o : sharedsorclass.cpp
- $(CC) $(CC_OPTIONS) sharedsorclass.cpp -c $(INCLUDE) -o ./sharedsorclass.o
-
-
-# Item # 130 -- sharedsorest --
-./sharedsorest.o : sharedsorest.cpp
- $(CC) $(CC_OPTIONS) sharedsorest.cpp -c $(INCLUDE) -o ./sharedsorest.o
-
-
-# Item # 131 -- sharedthetan --
-./sharedthetan.o : sharedthetan.cpp
- $(CC) $(CC_OPTIONS) sharedthetan.cpp -c $(INCLUDE) -o ./sharedthetan.o
-
-
-# Item # 132 -- sharedthetayc --
-./sharedthetayc.o : sharedthetayc.cpp
- $(CC) $(CC_OPTIONS) sharedthetayc.cpp -c $(INCLUDE) -o ./sharedthetayc.o
-
-
-# Item # 133 -- simpson --
-./simpson.o : simpson.cpp
- $(CC) $(CC_OPTIONS) simpson.cpp -c $(INCLUDE) -o ./simpson.o
-
-
-# Item # 134 -- singlelinkage --
-./singlelinkage.o : singlelinkage.cpp
- $(CC) $(CC_OPTIONS) singlelinkage.cpp -c $(INCLUDE) -o ./singlelinkage.o
-
-
-# Item # 135 -- sparsematrix --
-./sparsematrix.o : sparsematrix.cpp
- $(CC) $(CC_OPTIONS) sparsematrix.cpp -c $(INCLUDE) -o ./sparsematrix.o
-
-
-# Item # 136 -- summarycommand --
-./summarycommand.o : summarycommand.cpp
- $(CC) $(CC_OPTIONS) summarycommand.cpp -c $(INCLUDE) -o ./summarycommand.o
-
-
-# Item # 137 -- summarysharedcommand --
-./summarysharedcommand.o : summarysharedcommand.cpp
- $(CC) $(CC_OPTIONS) summarysharedcommand.cpp -c $(INCLUDE) -o ./summarysharedcommand.o
-
-
-# Item # 138 -- uvest --
-./uvest.o : uvest.cpp
- $(CC) $(CC_OPTIONS) uvest.cpp -c $(INCLUDE) -o ./uvest.o
-
-
-# Item # 139 -- validcalculator --
-./validcalculator.o : validcalculator.cpp
- $(CC) $(CC_OPTIONS) validcalculator.cpp -c $(INCLUDE) -o ./validcalculator.o
-
-
-# Item # 140 -- validparameter --
-./validparameter.o : validparameter.cpp
- $(CC) $(CC_OPTIONS) validparameter.cpp -c $(INCLUDE) -o ./validparameter.o
-
-
-# Item # 141 -- treenode --
-./treenode.o : treenode.cpp
- $(CC) $(CC_OPTIONS) treenode.cpp -c $(INCLUDE) -o ./treenode.o
-
-
-# Item # 142 -- readtreecommand --
-./readtreecommand.o : readtreecommand.cpp
- $(CC) $(CC_OPTIONS) readtreecommand.cpp -c $(INCLUDE) -o ./readtreecommand.o
-
-
-# Item # 143 -- reversecommand --
-./reversecommand.o : reversecommand.cpp
- $(CC) $(CC_OPTIONS) reversecommand.cpp -c $(INCLUDE) -o ./reversecommand.o
-
-
-# Item # 144 -- trimseqscommand --
-./trimseqscommand.o : trimseqscommand.cpp
- $(CC) $(CC_OPTIONS) trimseqscommand.cpp -c $(INCLUDE) -o ./trimseqscommand.o
-
-
-# Item # 145 -- slibshuff --
-./slibshuff.o : slibshuff.cpp
- $(CC) $(CC_OPTIONS) slibshuff.cpp -c $(INCLUDE) -o ./slibshuff.o
-
-
-# Item # 146 -- libshuff --
-./libshuff.o : libshuff.cpp
- $(CC) $(CC_OPTIONS) libshuff.cpp -c $(INCLUDE) -o ./libshuff.o
-
-
-# Item # 147 -- dlibshuff --
-./dlibshuff.o : dlibshuff.cpp
- $(CC) $(CC_OPTIONS) dlibshuff.cpp -c $(INCLUDE) -o ./dlibshuff.o
-
-
-# Item # 148 -- mergefilecommand --
-./mergefilecommand.o : mergefilecommand.cpp
- $(CC) $(CC_OPTIONS) mergefilecommand.cpp -c $(INCLUDE) -o ./mergefilecommand.o
-
-
-# Item # 149 -- coverage --
-./coverage.o : coverage.cpp
- $(CC) $(CC_OPTIONS) coverage.cpp -c $(INCLUDE) -o ./coverage.o
-
-
-# Item # 150 -- whittaker --
-./whittaker.o : whittaker.cpp
- $(CC) $(CC_OPTIONS) whittaker.cpp -c $(INCLUDE) -o ./whittaker.o
-
-
-# Item # 151 -- preclustercommand --
-./preclustercommand.o : preclustercommand.cpp
- $(CC) $(CC_OPTIONS) preclustercommand.cpp -c $(INCLUDE) -o ./preclustercommand.o
-
-
-# Item # 152 -- otuhierarchycommand --
-./otuhierarchycommand.o : otuhierarchycommand.cpp
- $(CC) $(CC_OPTIONS) otuhierarchycommand.cpp -c $(INCLUDE) -o ./otuhierarchycommand.o
-
-
-# Item # 153 -- setdircommand --
-./setdircommand.o : setdircommand.cpp
- $(CC) $(CC_OPTIONS) setdircommand.cpp -c $(INCLUDE) -o ./setdircommand.o
-
-
-# Item # 154 -- getgroupcommand --
-./getgroupcommand.o : getgroupcommand.cpp
- $(CC) $(CC_OPTIONS) getgroupcommand.cpp -c $(INCLUDE) -o ./getgroupcommand.o
-
-
-# Item # 155 -- getlabelcommand --
-./getlabelcommand.o : getlabelcommand.cpp
- $(CC) $(CC_OPTIONS) getlabelcommand.cpp -c $(INCLUDE) -o ./getlabelcommand.o
-
-
-# Item # 156 -- secondarystructurecommand --
-./secondarystructurecommand.o : secondarystructurecommand.cpp
- $(CC) $(CC_OPTIONS) secondarystructurecommand.cpp -c $(INCLUDE) -o ./secondarystructurecommand.o
-
-
-# Item # 157 -- mothurout --
-./mothurout.o : mothurout.cpp
- $(CC) $(CC_OPTIONS) mothurout.cpp -c $(INCLUDE) -o ./mothurout.o
-
-
-# Item # 158 -- parselistscommand --
-./parselistscommand.o : parselistscommand.cpp
- $(CC) $(CC_OPTIONS) parselistscommand.cpp -c $(INCLUDE) -o ./parselistscommand.o
-
-
-# Item # 159 -- readblast --
-./readblast.o : readblast.cpp
- $(CC) $(CC_OPTIONS) readblast.cpp -c $(INCLUDE) -o ./readblast.o
-
-
-# Item # 160 -- chimeracheckrdp --
-./chimeracheckrdp.o : chimeracheckrdp.cpp
- $(CC) $(CC_OPTIONS) chimeracheckrdp.cpp -c $(INCLUDE) -o ./chimeracheckrdp.o
-
-
-# Item # 161 -- hclustercommand --
-./hclustercommand.o : hclustercommand.cpp
- $(CC) $(CC_OPTIONS) hclustercommand.cpp -c $(INCLUDE) -o ./hclustercommand.o
-
-
-# Item # 162 -- hcluster --
-./hcluster.o : hcluster.cpp
- $(CC) $(CC_OPTIONS) hcluster.cpp -c $(INCLUDE) -o ./hcluster.o
-
-
-# Item # 163 -- getlistcountcommand --
-./getlistcountcommand.o : getlistcountcommand.cpp
- $(CC) $(CC_OPTIONS) getlistcountcommand.cpp -c $(INCLUDE) -o ./getlistcountcommand.o
-
-
-# Item # 164 -- readcluster --
-./readcluster.o : readcluster.cpp
- $(CC) $(CC_OPTIONS) readcluster.cpp -c $(INCLUDE) -o ./readcluster.o
-
-
-# Item # 165 -- ccode --
-./ccode.o : ccode.cpp
- $(CC) $(CC_OPTIONS) ccode.cpp -c $(INCLUDE) -o ./ccode.o
-
-
-# Item # 166 -- taxonomyequalizer --
-./taxonomyequalizer.o : taxonomyequalizer.cpp
- $(CC) $(CC_OPTIONS) taxonomyequalizer.cpp -c $(INCLUDE) -o ./taxonomyequalizer.o
-
-
-# Item # 167 -- phylotypecommand --
-./phylotypecommand.o : phylotypecommand.cpp
- $(CC) $(CC_OPTIONS) phylotypecommand.cpp -c $(INCLUDE) -o ./phylotypecommand.o
-
-
-# Item # 168 -- classifyseqscommand --
-./classifyseqscommand.o : classifyseqscommand.cpp
- $(CC) $(CC_OPTIONS) classifyseqscommand.cpp -c $(INCLUDE) -o ./classifyseqscommand.o
-
-
-# Item # 169 -- classify --
-./classify.o : classify.cpp
- $(CC) $(CC_OPTIONS) classify.cpp -c $(INCLUDE) -o ./classify.o
-
-
-# Item # 170 -- phylotree --
-./phylotree.o : phylotree.cpp
- $(CC) $(CC_OPTIONS) phylotree.cpp -c $(INCLUDE) -o ./phylotree.o
-
-
-# Item # 171 -- bayesian --
-./bayesian.o : bayesian.cpp
- $(CC) $(CC_OPTIONS) bayesian.cpp -c $(INCLUDE) -o ./bayesian.o
-
-
-# Item # 172 -- alignmentdb --
-./alignmentdb.o : alignmentdb.cpp
- $(CC) $(CC_OPTIONS) alignmentdb.cpp -c $(INCLUDE) -o ./alignmentdb.o
-
-
-# Item # 173 -- knn --
-./knn.o : knn.cpp
- $(CC) $(CC_OPTIONS) knn.cpp -c $(INCLUDE) -o ./knn.o
-
-
-# Item # 174 -- distancedb --
-./distancedb.o : distancedb.cpp
- $(CC) $(CC_OPTIONS) distancedb.cpp -c $(INCLUDE) -o ./distancedb.o
-
-
-# Item # 175 -- chimeraslayer --
-./chimeraslayer.o : chimeraslayer.cpp
- $(CC) $(CC_OPTIONS) chimeraslayer.cpp -c $(INCLUDE) -o ./chimeraslayer.o
-
-
-# Item # 176 -- slayer --
-./slayer.o : slayer.cpp
- $(CC) $(CC_OPTIONS) slayer.cpp -c $(INCLUDE) -o ./slayer.o
-
-
-# Item # 177 -- pcacommand --
-./pcacommand.o : pcacommand.cpp
- $(CC) $(CC_OPTIONS) pcacommand.cpp -c $(INCLUDE) -o ./pcacommand.o
-
-
-# Item # 178 -- formatcolumn --
-./formatcolumn.o : formatcolumn.cpp
- $(CC) $(CC_OPTIONS) formatcolumn.cpp -c $(INCLUDE) -o ./formatcolumn.o
-
-
-# Item # 179 -- formatphylip --
-./formatphylip.o : formatphylip.cpp
- $(CC) $(CC_OPTIONS) formatphylip.cpp -c $(INCLUDE) -o ./formatphylip.o
-
-
-# Item # 180 -- mgclustercommand --
-./mgclustercommand.o : mgclustercommand.cpp
- $(CC) $(CC_OPTIONS) mgclustercommand.cpp -c $(INCLUDE) -o ./mgclustercommand.o
-
-
-# Item # 181 -- getsharedotucommand --
-./getsharedotucommand.o : getsharedotucommand.cpp
- $(CC) $(CC_OPTIONS) getsharedotucommand.cpp -c $(INCLUDE) -o ./getsharedotucommand.o
-
-
-# Item # 182 -- maligner --
-./maligner.o : maligner.cpp
- $(CC) $(CC_OPTIONS) maligner.cpp -c $(INCLUDE) -o ./maligner.o
-
-
-# Item # 183 -- chimerarealigner --
-./chimerarealigner.o : chimerarealigner.cpp
- $(CC) $(CC_OPTIONS) chimerarealigner.cpp -c $(INCLUDE) -o ./chimerarealigner.o
-
-
-# Item # 184 -- bergerparker --
-./bergerparker.o : bergerparker.cpp
- $(CC) $(CC_OPTIONS) bergerparker.cpp -c $(INCLUDE) -o ./bergerparker.o
-
-
-# Item # 185 -- bstick --
-./bstick.o : bstick.cpp
- $(CC) $(CC_OPTIONS) bstick.cpp -c $(INCLUDE) -o ./bstick.o
-
-
-# Item # 186 -- sharedkstest --
-./sharedkstest.o : sharedkstest.cpp
- $(CC) $(CC_OPTIONS) sharedkstest.cpp -c $(INCLUDE) -o ./sharedkstest.o
-
-
-# Item # 187 -- qstat --
-./qstat.o : qstat.cpp
- $(CC) $(CC_OPTIONS) qstat.cpp -c $(INCLUDE) -o ./qstat.o
-
-
-# Item # 188 -- shen --
-./shen.o : shen.cpp
- $(CC) $(CC_OPTIONS) shen.cpp -c $(INCLUDE) -o ./shen.o
-
-
-# Item # 189 -- logsd --
-./logsd.o : logsd.cpp
- $(CC) $(CC_OPTIONS) logsd.cpp -c $(INCLUDE) -o ./logsd.o
-
-
-# Item # 190 -- geom --
-./geom.o : geom.cpp
- $(CC) $(CC_OPTIONS) geom.cpp -c $(INCLUDE) -o ./geom.o
-
-# Item # 191 -- parsesffcommand --
-./parsesffcommand.o : parsesffcommand.cpp
- $(CC) $(CC_OPTIONS) parsesffcommand.cpp -c $(INCLUDE) -o ./parsesffcommand.o
-
-# Item # 192 -- chimeraccodecommand --
-./chimeraccodecommand.o : chimeraccodecommand.cpp
- $(CC) $(CC_OPTIONS) chimeraccodecommand.cpp -c $(INCLUDE) -o ./chimeraccodecommand.o
-
-# Item # 193 -- chimeracheckcommand --
-./chimeracheckcommand.o : chimeracheckcommand.cpp
- $(CC) $(CC_OPTIONS) chimeracheckcommand.cpp -c $(INCLUDE) -o ./chimeracheckcommand.o
-
-
-# Item # 194 -- chimeraslayercommand --
-./chimeraslayercommand.o : chimeraslayercommand.cpp
- $(CC) $(CC_OPTIONS) chimeraslayercommand.cpp -c $(INCLUDE) -o ./chimeraslayercommand.o
-
-# Item # 195 -- chimerapintailcommand --
-./chimerapintailcommand.o : chimerapintailcommand.cpp
- $(CC) $(CC_OPTIONS) chimerapintailcommand.cpp -c $(INCLUDE) -o ./chimerapintailcommand.o
-
-# Item # 196 -- chimerabellerophoncommand --
-./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp
- $(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o
-
-# Item # 197 -- phylosummary --
-./phylosummary.o : phylosummary.cpp
- $(CC) $(CC_OPTIONS) phylosummary.cpp -c $(INCLUDE) -o ./phylosummary.o
-
-# Item # 198 -- setlogfilecommand --
-./setlogfilecommand.o : setlogfilecommand.cpp
- $(CC) $(CC_OPTIONS) setlogfilecommand.cpp -c $(INCLUDE) -o ./setlogfilecommand.o
-
-# Item # 199 -- phylodiversity --
-./phylodiversity.o : phylodiversity.cpp
- $(CC) $(CC_OPTIONS) phylodiversity.cpp -c $(INCLUDE) -o ./phylodiversity.o
-
-# Item # 200 -- phylodiversitycommand --
-./phylodiversitycommand.o : phylodiversitycommand.cpp
- $(CC) $(CC_OPTIONS) phylodiversitycommand.cpp -c $(INCLUDE) -o ./phylodiversitycommand.o
-
-# Item # 201 -- makegroupcommand --
-./makegroupcommand.o : makegroupcommand.cpp
- $(CC) $(CC_OPTIONS) makegroupcommand.cpp -c $(INCLUDE) -o ./makegroupcommand.o
-
-# Item # 202 -- chopseqscommand --
-./chopseqscommand.o : chopseqscommand.cpp
- $(CC) $(CC_OPTIONS) chopseqscommand.cpp -c $(INCLUDE) -o ./chopseqscommand.o
-
-# Item # 203 -- clearcutcommand --
-./clearcutcommand.o : clearcutcommand.cpp
- $(CC) $(CC_OPTIONS) clearcutcommand.cpp -c $(INCLUDE) -o ./clearcutcommand.o
-
-# Item # 204 -- catchallcommand --
-./catchallcommand.o : catchallcommand.cpp
- $(CC) $(CC_OPTIONS) catchallcommand.cpp -c $(INCLUDE) -o ./catchallcommand.o
-
-# Item # 205 -- splitabundcommand --
-./splitabundcommand.o : splitabundcommand.cpp
- $(CC) $(CC_OPTIONS) splitabundcommand.cpp -c $(INCLUDE) -o ./splitabundcommand.o
-
-# Item # 206 -- splitmatrix --
-./splitmatrix.o : splitmatrix.cpp
- $(CC) $(CC_OPTIONS) splitmatrix.cpp -c $(INCLUDE) -o ./splitmatrix.o
-
-# Item # 207 -- clustersplit --
-./clustersplitcommand.o : clustersplitcommand.cpp
- $(CC) $(CC_OPTIONS) clustersplitcommand.cpp -c $(INCLUDE) -o ./clustersplitcommand.o
-
-# Item # 208 -- classifyotu --
-./classifyotucommand.o : classifyotucommand.cpp
- $(CC) $(CC_OPTIONS) classifyotucommand.cpp -c $(INCLUDE) -o ./classifyotucommand.o
-
-# Item # 209 -- weightedlinkage --
-./weightedlinkage.o : weightedlinkage.cpp
- $(CC) $(CC_OPTIONS) weightedlinkage.cpp -c $(INCLUDE) -o ./weightedlinkage.o
-
-# Item # 210 -- degapseqscommand --
-./degapseqscommand.o : degapseqscommand.cpp
- $(CC) $(CC_OPTIONS) degapseqscommand.cpp -c $(INCLUDE) -o ./degapseqscommand.o
-
-# Item # 211 -- getrelabundcommand --
-./getrelabundcommand.o : getrelabundcommand.cpp
- $(CC) $(CC_OPTIONS) getrelabundcommand.cpp -c $(INCLUDE) -o ./getrelabundcommand.o
-
-##### END RUN ####
+###################################################\r
+#\r
+# Makefile for mothur\r
+# Created: June 29, 2010\r
+#\r
+###################################################\r
+\r
+#\r
+# Macros\r
+#\r
+\r
+# Optimize to level 3:\r
+\r
+CXXFLAGS += -O3\r
+\r
+CYGWIN_BUILD ?= no\r
+ifeq ($(strip $(CYGWIN_BUILD)),yes)\r
+ CXXFLAGS += -mno-cygwin\r
+ LDFLAGS += -mno-cygwin \r
+#-lpsapi\r
+endif\r
+\r
+64BIT_VERSION ?= yes\r
+\r
+ifeq ($(strip $(64BIT_VERSION)),yes)\r
+ TARGET_ARCH += -arch x86_64\r
+endif\r
+\r
+# if you do not want to use the readline library, set this to no.\r
+# make sure you have the library installed\r
+\r
+USEREADLINE ?= yes\r
+\r
+ifeq ($(strip $(USEREADLINE)),yes)\r
+ CXXFLAGS += -DUSE_READLINE\r
+ LDFLAGS += \\r
+ -lreadline\\r
+ -lncurses\\r
+ -L../readline-6.0\r
+endif\r
+\r
+USEMPI ?= no\r
+\r
+ifeq ($(strip $(USEMPI)),yes)\r
+ CXX = mpic++\r
+ CXXFLAGS += -DUSE_MPI\r
+endif\r
+\r
+#\r
+# INCLUDE directories for mothur\r
+#\r
+\r
+ CXXFLAGS += -I.\r
+\r
+#\r
+# Get the list of all .cpp files, rename to .o files\r
+#\r
+\r
+OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))\r
+\r
+mothur : $(OBJECTS)\r
+ $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS)\r
+\r
+install : mothur\r
+ cp mothur ../Release/mothur\r
+\r
+clean :\r
+ @rm -f $(OBJECTS)\r
-/*\r
- * m->mothurOut.cpp\r
- * Mothur\r
- *\r
- * Created by westcott on 2/25/10.\r
- * Copyright 2010 Schloss Lab. All rights reserved.\r
- *\r
- */\r
-\r
-#include "mothurout.h"\r
-\r
-/******************************************************/\r
-MothurOut* MothurOut::getInstance() {\r
- if( _uniqueInstance == 0) {\r
- _uniqueInstance = new MothurOut();\r
- }\r
- return _uniqueInstance;\r
-}\r
-/*********************************************************************************************/\r
-void MothurOut::setFileName(string filename) {\r
- try {\r
- logFileName = filename;\r
- \r
- #ifdef USE_MPI\r
- int pid;\r
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); \r
- \r
- if (pid == 0) { //only one process should output to screen\r
- #endif\r
- \r
- openOutputFile(filename, out);\r
- \r
- #ifdef USE_MPI\r
- }\r
- #endif\r
- }\r
- catch(exception& e) {\r
- errorOut(e, "MothurOut", "setFileName");\r
- exit(1);\r
- }\r
-}\r
-/*********************************************************************************************/\r
-void MothurOut::closeLog() {\r
- try {\r
- \r
- #ifdef USE_MPI\r
- int pid;\r
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); \r
- \r
- if (pid == 0) { //only one process should output to screen\r
- #endif\r
- \r
- out.close();\r
- \r
- #ifdef USE_MPI\r
- }\r
- #endif\r
- }\r
- catch(exception& e) {\r
- errorOut(e, "MothurOut", "closeLog");\r
- exit(1);\r
- }\r
-}\r
-\r
-/*********************************************************************************************/\r
-MothurOut::~MothurOut() {\r
- try {\r
- _uniqueInstance = 0;\r
- \r
- }\r
- catch(exception& e) {\r
- errorOut(e, "MothurOut", "MothurOut");\r
- exit(1);\r
- }\r
-}\r
-/*********************************************************************************************/\r
-void MothurOut::mothurOut(string output) {\r
- try {\r
- \r
- #ifdef USE_MPI\r
- int pid;\r
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); \r
- \r
- if (pid == 0) { //only one process should output to screen\r
- #endif\r
- \r
- cout << output;\r
- out << output;\r
- \r
- #ifdef USE_MPI\r
- }\r
- #endif\r
- }\r
- catch(exception& e) {\r
- errorOut(e, "MothurOut", "MothurOut");\r
- exit(1);\r
- }\r
-}\r
-/*********************************************************************************************/\r
-void MothurOut::mothurOutEndLine() {\r
- try {\r
- #ifdef USE_MPI\r
- int pid;\r
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); \r
- \r
- if (pid == 0) { //only one process should output to screen\r
- #endif\r
- \r
- cout << endl;\r
- out << endl;\r
- \r
- #ifdef USE_MPI\r
- }\r
- #endif\r
- }\r
- catch(exception& e) {\r
- errorOut(e, "MothurOut", "MothurOutEndLine");\r
- exit(1);\r
- }\r
-}\r
-/*********************************************************************************************/\r
-void MothurOut::mothurOutJustToLog(string output) {\r
- try {\r
- #ifdef USE_MPI\r
- int pid;\r
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); \r
- \r
- if (pid == 0) { //only one process should output to screen\r
- #endif\r
- \r
- out << output;\r
- \r
- #ifdef USE_MPI\r
- }\r
- #endif\r
- }\r
- catch(exception& e) {\r
- errorOut(e, "MothurOut", "MothurOutJustToLog");\r
- exit(1);\r
- }\r
-}\r
-/*********************************************************************************************/\r
-void MothurOut::errorOut(exception& e, string object, string function) {\r
- mothurOut("Error: ");\r
- mothurOut(toString(e.what()));\r
- mothurOut(" has occurred in the " + object + " class function " + function + ". Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.");\r
- mothurOutEndLine();\r
-}\r
-/*********************************************************************************************/\r
-\r
-\r
-\r
-\r
-\r
+/*
+ * m->mothurOut.cpp
+ * Mothur
+ *
+ * Created by westcott on 2/25/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mothurout.h"
+
+/******************************************************/
+MothurOut* MothurOut::getInstance() {
+ if( _uniqueInstance == 0) {
+ _uniqueInstance = new MothurOut();
+ }
+ return _uniqueInstance;
+}
+/*********************************************************************************************/
+void MothurOut::setFileName(string filename) {
+ try {
+ logFileName = filename;
+
+ #ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if (pid == 0) { //only one process should output to screen
+ #endif
+
+ openOutputFile(filename, out);
+
+ #ifdef USE_MPI
+ }
+ #endif
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "setFileName");
+ exit(1);
+ }
+}
+/*********************************************************************************************/
+void MothurOut::closeLog() {
+ try {
+
+ #ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if (pid == 0) { //only one process should output to screen
+ #endif
+
+ out.close();
+
+ #ifdef USE_MPI
+ }
+ #endif
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "closeLog");
+ exit(1);
+ }
+}
+
+/*********************************************************************************************/
+MothurOut::~MothurOut() {
+ try {
+ _uniqueInstance = 0;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "MothurOut");
+ exit(1);
+ }
+}
+/*********************************************************************************************/
+void MothurOut::mothurOut(string output) {
+ try {
+
+ #ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if (pid == 0) { //only one process should output to screen
+ #endif
+
+ cout << output;
+ out << output;
+
+ #ifdef USE_MPI
+ }
+ #endif
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "MothurOut");
+ exit(1);
+ }
+}
+/*********************************************************************************************/
+void MothurOut::mothurOutEndLine() {
+ try {
+ #ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if (pid == 0) { //only one process should output to screen
+ #endif
+
+ cout << endl;
+ out << endl;
+
+ #ifdef USE_MPI
+ }
+ #endif
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "MothurOutEndLine");
+ exit(1);
+ }
+}
+/*********************************************************************************************/
+void MothurOut::mothurOutJustToLog(string output) {
+ try {
+ #ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if (pid == 0) { //only one process should output to screen
+ #endif
+
+ out << output;
+
+ #ifdef USE_MPI
+ }
+ #endif
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "MothurOutJustToLog");
+ exit(1);
+ }
+}
+/*********************************************************************************************/
+void MothurOut::errorOut(exception& e, string object, string function) {
+ double vm, rss;
+ mem_usage(vm, rss);
+
+ mothurOut("Error: ");
+ mothurOut(toString(e.what()));
+ mothurOut(" has occurred in the " + object + " class function " + function + ". Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.");
+ mothurOutEndLine();
+}
+/*********************************************************************************************/
+//The following was originally from http://stackoverflow.com/questions/669438/how-to-get-memory-usage-at-run-time-in-c
+// process_mem_usage(double &, double &) - takes two doubles by reference,
+// attempts to read the system-dependent data for a process' virtual memory
+// size and resident set size, and return the results in KB.
+//
+// On failure, returns 0.0, 0.0
+int MothurOut::mem_usage(double& vm_usage, double& resident_set) {
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+
+ vm_usage = 0.0;
+ resident_set = 0.0;
+
+ // 'file' stat seems to give the most reliable results
+ //
+ ifstream stat_stream("/proc/self/stat",ios_base::in);
+
+ // dummy vars for leading entries in stat that we don't care about
+ //
+ string pid, comm, state, ppid, pgrp, session, tty_nr;
+ string tpgid, flags, minflt, cminflt, majflt, cmajflt;
+ string utime, stime, cutime, cstime, priority, nice;
+ string O, itrealvalue, starttime;
+
+ // the two fields we want
+ //
+ unsigned long vsize;
+ long rss;
+
+ stat_stream >> pid >> comm >> state >> ppid >> pgrp >> session >> tty_nr
+ >> tpgid >> flags >> minflt >> cminflt >> majflt >> cmajflt
+ >> utime >> stime >> cutime >> cstime >> priority >> nice
+ >> O >> itrealvalue >> starttime >> vsize >> rss; // don't care about the rest
+
+ long page_size_kb = sysconf(_SC_PAGE_SIZE) / 1024; // in case x86-64 is configured to use 2MB pages
+ vm_usage = vsize / 1024.0;
+ resident_set = rss * page_size_kb;
+
+ mothurOut("Memory Usage: vm = " + toString(vm_usage) + " rss = " + toString(resident_set) + "\n");
+ return 0;
+
+ #else
+/* //windows memory usage
+ // Get the list of process identifiers.
+ DWORD aProcesses[1024], cbNeeded, cProcesses;
+
+ if ( !EnumProcesses( aProcesses, sizeof(aProcesses), &cbNeeded ) ){ return 1; }
+
+ // Calculate how many process identifiers were returned.
+ cProcesses = cbNeeded / sizeof(DWORD);
+
+ // Print the memory usage for each process
+ for (int i = 0; i < cProcesses; i++ ) {
+ DWORD processID = aProcesses[i];
+
+ PROCESS_MEMORY_COUNTERS pmc;
+
+ HANDLE hProcess = OpenProcess((PROCESS_QUERY_INFORMATION | PROCESS_VM_READ), FALSE, processID);
+
+ // Print the process identifier.
+ printf( "\nProcess ID: %u\n", processID);
+
+ if (NULL != hProcess) {
+
+ if ( GetProcessMemoryInfo( hProcess, &pmc, sizeof(pmc)) ) {
+ printf( "\tPageFaultCount: 0x%08X\n", pmc.PageFaultCount );
+ printf( "\tPeakWorkingSetSize: 0x%08X\n", pmc.PeakWorkingSetSize );
+ printf( "\tWorkingSetSize: 0x%08X\n", pmc.WorkingSetSize );
+ printf( "\tQuotaPeakPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakPagedPoolUsage );
+ printf( "\tQuotaPagedPoolUsage: 0x%08X\n", pmc.QuotaPagedPoolUsage );
+ printf( "\tQuotaPeakNonPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakNonPagedPoolUsage );
+ printf( "\tQuotaNonPagedPoolUsage: 0x%08X\n", pmc.QuotaNonPagedPoolUsage );
+ printf( "\tPagefileUsage: 0x%08X\n", pmc.PagefileUsage );
+ printf( "\tPeakPagefileUsage: 0x%08X\n", pmc.PeakPagefileUsage );
+ }
+ CloseHandle(hProcess);
+ }
+ }
+*/
+ return 0;
+
+ #endif
+}
+/*********************************************************************************************/
+
+
+
+
+
try {
abort = false;
+ comboStarts = 0;
//allow user to run help
if(option == "help") { help(); abort = true; }
for(int i=0;i<fastaFileNames.size();i++){
- ifstream inFASTA;
- string seqName;
- //openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
- openInputFile(fastaFileNames[i], inFASTA);
- ofstream outGroups;
- string outGroupFilename = outputDir + getRootName(getSimpleName(fastaFileNames[i])) + "groups";
- openOutputFile(outGroupFilename, outGroups);
- //openOutputFile(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups", outGroups);
- outputNames.push_back(outGroupFilename);
-
- while(!inFASTA.eof()){
- if(inFASTA.get() == '>'){
- inFASTA >> seqName;
- outGroups << seqName << '\t' << groupVector[i] << endl;
+ if (isBlank(fastaFileNames[i])) { remove(fastaFileNames[i].c_str()); }
+ else {
+ ifstream inFASTA;
+ string seqName;
+ //openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
+ openInputFile(fastaFileNames[i], inFASTA);
+ ofstream outGroups;
+ string outGroupFilename = outputDir + getRootName(getSimpleName(fastaFileNames[i])) + "groups";
+ openOutputFile(outGroupFilename, outGroups);
+ //openOutputFile(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups", outGroups);
+ outputNames.push_back(outGroupFilename);
+
+ string thisGroup = "";
+ if (i > comboStarts) {
+ map<string, int>::iterator itCombo;
+ for(itCombo=combos.begin();itCombo!=combos.end(); itCombo++){
+ if(itCombo->second == i){ thisGroup = itCombo->first; combos.erase(itCombo); break; }
+ }
+ }else{ thisGroup = groupVector[i]; }
+
+ while(!inFASTA.eof()){
+ if(inFASTA.get() == '>'){
+ inFASTA >> seqName;
+ outGroups << seqName << '\t' << thisGroup << endl;
+ }
+ while (!inFASTA.eof()) { char c = inFASTA.get(); if (c == 10 || c == 13){ break; } }
}
- while (!inFASTA.eof()) { char c = inFASTA.get(); if (c == 10 || c == 13){ break; } }
+ outGroups.close();
+ inFASTA.close();
}
- outGroups.close();
- inFASTA.close();
}
if (m->control_pressed) {
string origSeq = currSeq.getUnaligned();
if (origSeq != "") {
- int group;
+ int groupBar, groupPrime;
string trashCode = "";
int currentSeqsDiffs = 0;
}
if(barcodes.size() != 0){
- success = stripBarcode(currSeq, group);
+ success = stripBarcode(currSeq, groupBar);
if(success > bdiffs){ trashCode += 'b'; }
else{ currentSeqsDiffs += success; }
}
if(numFPrimers != 0){
- success = stripForward(currSeq);
+ success = stripForward(currSeq, groupPrime);
if(success > pdiffs){ trashCode += 'f'; }
else{ currentSeqsDiffs += success; }
}
currSeq.setAligned(currSeq.getUnaligned());
currSeq.printSequence(outFASTA);
if(barcodes.size() != 0){
- outGroups << currSeq.getName() << '\t' << groupVector[group] << endl;
+ string thisGroup = groupVector[groupBar];
+ int indexToFastaFile = groupBar;
+ if (primers.size() != 0){
+ //does this primer have a group
+ if (groupVector[groupPrime] != "") {
+ thisGroup += "." + groupVector[groupPrime];
+ indexToFastaFile = combos[thisGroup];
+ }
+ }
+ outGroups << currSeq.getName() << '\t' << thisGroup << endl;
if(allFiles){
- currSeq.printSequence(*fastaFileNames[group]);
+ currSeq.printSequence(*fastaFileNames[indexToFastaFile]);
}
}
}
string type, oligo, group;
int index=0;
+ //int indexPrimer = 0;
while(!inOligos.eof()){
inOligos >> type;
}
if(type == "forward"){
- forPrimer.push_back(oligo);
+ group = "";
+
+ // get rest of line in case there is a primer name
+ while (!inOligos.eof()) {
+ char c = inOligos.get();
+ if (c == 10 || c == 13){ break; }
+ else if (c == 32 || c == 9){;} //space or tab
+ else { group += c; }
+ }
+
+ //check for repeat barcodes
+ map<string, int>::iterator itPrime = primers.find(oligo);
+ if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
+
+ primers[oligo]=index; index++;
+ groupVector.push_back(group);
+
+ if(allFiles){
+ if (group != "") { //there is a group for this primer
+ outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + toString(index) + "." + group + ".fasta"));
+ outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + toString(index) + "." + group + ".fasta"));
+ }
+ }
}
else if(type == "reverse"){
Sequence oligoRC("reverse", oligo);
}
else if(type == "barcode"){
inOligos >> group;
+
+ //check for repeat barcodes
+ map<string, int>::iterator itBar = barcodes.find(oligo);
+ if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
+
barcodes[oligo]=index; index++;
groupVector.push_back(group);
if(allFiles){
- //outFASTAVec.push_back(new ofstream((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta").c_str(), ios::ate));
outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + toString(index) + "." + group + ".fasta"));
outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + toString(index) + "." + group + ".fasta"));
}
}else{ m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
}
+ gobble(inOligos);
}
inOligos.close();
- numFPrimers = forPrimer.size();
+ //add in potential combos
+ if(allFiles){
+ comboStarts = outFASTAVec.size()-1;
+ for (map<string, int>::iterator itBar = barcodes.begin(); itBar != barcodes.end(); itBar++) {
+ for (map<string, int>::iterator itPrime = primers.begin(); itPrime != primers.end(); itPrime++) {
+ if (groupVector[itPrime->second] != "") { //there is a group for this primer
+ outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + toString(itBar->second) + "." + groupVector[itBar->second] + "." + toString(itPrime->second) + "." + groupVector[itPrime->second] + ".fasta"));
+ outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + toString(itBar->second) + "." + groupVector[itBar->second] + "." + toString(itPrime->second) + "." + groupVector[itPrime->second] + ".fasta"));
+ combos[(groupVector[itBar->second] + "." + groupVector[itPrime->second])] = outFASTAVec.size()-1;
+ }
+ }
+ }
+ }
+
+ numFPrimers = primers.size();
numRPrimers = revPrimer.size();
}
//***************************************************************************************************************
-int TrimSeqsCommand::stripForward(Sequence& seq){
+int TrimSeqsCommand::stripForward(Sequence& seq, int& group){
try {
string rawSequence = seq.getUnaligned();
int success = pdiffs + 1; //guilty until proven innocent
//can you find the primer
- for(int i=0;i<numFPrimers;i++){
- string oligo = forPrimer[i];
-
- if(rawSequence.length() < oligo.length()){
- success = pdiffs + 1;
- break;
+ for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
+ string oligo = it->first;
+ if(rawSequence.length() < oligo.length()){ //let's just assume that the primers are the same length
+ success = pdiffs + 10; //if the sequence is shorter than the barcode then bail out
+ break;
}
if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
+ group = it->second;
seq.setUnaligned(rawSequence.substr(oligo.length()));
success = 0;
break;
}
}
-
+
//if you found the barcode or if you don't want to allow for diffs
// cout << success;
if ((pdiffs == 0) || (success == 0)) { return success; }
int maxLength = 0;
Alignment* alignment;
- if (numFPrimers > 0) {
+ if (primers.size() > 0) {
+ map<string,int>::iterator it=primers.begin();
- for(int i=0;i<numFPrimers;i++){
- if(forPrimer[i].length() > maxLength){
- maxLength = forPrimer[i].length();
+ for(it;it!=primers.end();it++){
+ if(it->first.length() > maxLength){
+ maxLength = it->first.length();
}
}
alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));
//can you find the barcode
int minDiff = 1e6;
int minCount = 1;
+ int minGroup = -1;
int minPos = 0;
- for(int i=0;i<numFPrimers;i++){
- string oligo = forPrimer[i];
+ for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
+ string oligo = it->first;
+// int length = oligo.length();
if(rawSequence.length() < maxLength){
success = pdiffs + 100;
}
oligo = oligo.substr(0,alnLength);
temp = temp.substr(0,alnLength);
-
+
int newStart=0;
int numDiff = countDiffs(oligo, temp);
+
+// cout << oligo << '\t' << temp << '\t' << numDiff << endl;
+
if(numDiff < minDiff){
minDiff = numDiff;
minCount = 1;
+ minGroup = it->second;
minPos = 0;
for(int i=0;i<alnLength;i++){
if(temp[i] != '-'){
}
}
- if(minDiff > pdiffs) { success = minDiff; }
- else if(minCount > 1) { success = pdiffs + 10; }
- else{
+
+ if(minDiff > pdiffs) { success = minDiff; } //no good matches
+ else if(minCount > 1) { success = pdiffs + 10; } //can't tell the difference between multiple primers
+ else{ //use the best match
+ group = minGroup;
seq.setUnaligned(rawSequence.substr(minPos));
success = minDiff;
}
if (alignment != NULL) { delete alignment; }
}
+
return success;
}
projects / mothur.git / commitdiff