From 62568a297aaf939ab753334f17abde82ec8e8531 Mon Sep 17 00:00:00 2001 From: westcott Date: Thu, 27 May 2010 12:47:59 +0000 Subject: [PATCH] changes to chop.seqs --- bayesian.cpp | 12 +- chopseqscommand.cpp | 127 +- chopseqscommand.h | 6 +- classify.cpp | 7 +- clustersplitcommand.cpp | 9 +- commandfactory.cpp | 4 +- makefile | 3402 +++++++++++++++++++-------------------- mothur.cpp | 4 +- phylotree.cpp | 95 +- phylotree.h | 10 +- 10 files changed, 1929 insertions(+), 1747 deletions(-) diff --git a/bayesian.cpp b/bayesian.cpp index 63f8716..57b8e20 100644 --- a/bayesian.cpp +++ b/bayesian.cpp @@ -213,7 +213,7 @@ string Bayesian::getTaxonomy(Sequence* seq) { int index = getMostProbableTaxonomy(queryKmers); if (m->control_pressed) { return tax; } - +//cout << seq->getName() << '\t' << index << endl; //bootstrap - to set confidenceScore int numToSelect = queryKmers.size() / 8; tax = bootstrapResults(queryKmers, index, numToSelect); @@ -249,10 +249,10 @@ string Bayesian::bootstrapResults(vector kmers, int tax, int numToSelect) { //get taxonomy int newTax = getMostProbableTaxonomy(temp); - TaxNode taxonomy = phyloTree->get(newTax); - + TaxNode taxonomyTemp = phyloTree->get(newTax); + //add to confidence results - while (taxonomy.level != 0) { //while you are not at the root + while (taxonomyTemp.level != 0) { //while you are not at the root itBoot2 = confidenceScores.find(newTax); //is this a classification we already have a count on @@ -262,8 +262,8 @@ string Bayesian::bootstrapResults(vector kmers, int tax, int numToSelect) { confidenceScores[newTax]++; } - newTax = taxonomy.parent; - taxonomy = phyloTree->get(taxonomy.parent); + newTax = taxonomyTemp.parent; + taxonomyTemp = phyloTree->get(newTax); } } diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp index adf0910..9020d2b 100644 --- a/chopseqscommand.cpp +++ b/chopseqscommand.cpp @@ -21,7 +21,7 @@ ChopSeqsCommand::ChopSeqsCommand(string option) { else { //valid paramters for this command - string Array[] = {"fasta","end","outputdir","inputdir"}; + string Array[] = {"fasta","end","fromend","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -57,13 +57,14 @@ ChopSeqsCommand::ChopSeqsCommand(string option) { if (fastafile == "not open") { abort = true; } else if (fastafile == "not found") { m->mothurOut("You must provide a fasta file."); m->mothurOutEndLine(); abort = true; } - string temp = validParameter.validFile(parameters, "end", false); - if (temp == "not found") { m->mothurOut("You must provide an end for the chops.seqs command."); m->mothurOutEndLine(); abort = true; } - else { - convert(temp, end); - if (end < 0) { m->mothurOut("End must be positive."); m->mothurOutEndLine(); abort = true; } - } - + string temp = validParameter.validFile(parameters, "end", false); if (temp == "not found") { temp = "0"; } + convert(temp, end); + + temp = validParameter.validFile(parameters, "fromend", false); if (temp == "not found") { temp = "0"; } + convert(temp, fromend); + + if ((end == 0) && (fromend == 0)) { m->mothurOut("You must provide either end or fromend for the chops.seqs command."); m->mothurOutEndLine(); abort = true; } + if ((end != 0) && (fromend != 0)) { m->mothurOut("You must provide either end or fromend for the chops.seqs command, not both."); m->mothurOutEndLine(); abort = true; } } } @@ -77,8 +78,10 @@ ChopSeqsCommand::ChopSeqsCommand(string option) { void ChopSeqsCommand::help(){ try { m->mothurOut("The chop.seqs command reads a fasta file and outputs a .chop.fasta with sequences trimmed to the end position.\n"); - m->mothurOut("The chop.seqs command parameters are fasta and end, both are required.\n"); + m->mothurOut("The chop.seqs command parameters are fasta, end and fromend, fasta is required.\n"); m->mothurOut("The chop.seqs command should be in the following format: chop.seqs(fasta=yourFasta, end=yourEnd).\n"); + m->mothurOut("The end parameter allows you to specify an end base position for your sequences, default = 0.\n"); + m->mothurOut("The fromend parameter allows you to remove the last X bases from the end of the sequence, default = 0.\n"); m->mothurOut("Example chop.seqs(fasta=amazon.fasta, end=200).\n"); m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n"); } @@ -96,38 +99,53 @@ int ChopSeqsCommand::execute(){ if (abort == true) { return 0; } string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "chop.fasta"; + string outputFileNameAccnos = outputDir + getRootName(getSimpleName(fastafile)) + "chop.accnos"; ofstream out; openOutputFile(outputFileName, out); + ofstream outAcc; + openOutputFile(outputFileNameAccnos, outAcc); + ifstream in; openInputFile(fastafile, in); - while (!in.eof()) { + bool wroteAccnos = false; - Sequence seq(in, "no align"); + while (!in.eof()) { + + Sequence seq(in); - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); outAcc.close(); remove(outputFileName.c_str()); remove(outputFileNameAccnos.c_str()); return 0; } if (seq.getName() != "") { - string temp = seq.getUnaligned(); - - //output sequence name - out << ">" << seq.getName() << endl; - - //if needed trim sequence - if (temp.length() > end) { temp = temp.substr(0, end); } + string newSeqString = ""; + if (seq.getIsAligned()) { //sequence is aligned + newSeqString = getChoppedAligned(seq); + }else{ + newSeqString = getChoppedUnaligned(seq); + } - //output trimmed sequence - out << temp << endl; + //output trimmed sequence + if (newSeqString != "") { + out << ">" << seq.getName() << endl << newSeqString << endl; + }else{ + outAcc << seq.getName() << endl; + wroteAccnos = true; + } } } in.close(); out.close(); + outAcc.close(); m->mothurOutEndLine(); m->mothurOut("Output File Name: "); m->mothurOutEndLine(); m->mothurOut(outputFileName); m->mothurOutEndLine(); + + if (wroteAccnos) { m->mothurOut(outputFileNameAccnos); m->mothurOutEndLine(); } + else { remove(outputFileNameAccnos.c_str()); } + m->mothurOutEndLine(); return 0; @@ -138,7 +156,74 @@ int ChopSeqsCommand::execute(){ exit(1); } } +//********************************************************************************************************************** +string ChopSeqsCommand::getChoppedUnaligned(Sequence seq) { + try { + string temp = seq.getUnaligned(); + + //if needed trim sequence + if (end != 0) { + if (temp.length() > end) { temp = temp.substr(0, end); } + else { temp = ""; } + }else { //you are using fromend + if (temp.length() > fromend) { temp = temp.substr(0, (temp.length()-fromend)); } + else { temp = ""; } //sequence too short + } + + return temp; + } + catch(exception& e) { + m->errorOut(e, "ChopSeqsCommand", "getChoppedUnaligned"); + exit(1); + } +} +//********************************************************************************************************************** +string ChopSeqsCommand::getChoppedAligned(Sequence seq) { + try { + string temp = seq.getAligned(); + string tempUnaligned = seq.getUnaligned(); + + //if needed trim sequence + if (end != 0) { + if (tempUnaligned.length() > end) { //you have enough bases to remove some + + int stopSpot = 0; + int numBases = 0; + + for (int i = 0; i < temp.length(); i++) { + if(isalpha(temp[i])) { numBases++; } + if (numBases >= end) { stopSpot = i; break; } + } + + temp = temp.substr(0, stopSpot); + }else { temp = ""; } //sequence too short + + }else { //you are using fromend + + if (tempUnaligned.length() > fromend) { + + int stopSpot = 0; + int numBases = 0; + + for (int i = (temp.length()-1); i >= 0; i--) { + if(isalpha(temp[i])) { numBases++; } + + if (numBases >= fromend) { stopSpot = i; break; } + } + + temp = temp.substr(0, stopSpot); + } + else { temp = ""; } //sequence too short + } + + return temp; + } + catch(exception& e) { + m->errorOut(e, "ChopSeqsCommand", "getChoppedUnaligned"); + exit(1); + } +} //********************************************************************************************************************** diff --git a/chopseqscommand.h b/chopseqscommand.h index 5d8d6c4..2da134e 100644 --- a/chopseqscommand.h +++ b/chopseqscommand.h @@ -12,6 +12,7 @@ #include "command.hpp" +#include "sequence.hpp" class ChopSeqsCommand : public Command { @@ -25,7 +26,10 @@ class ChopSeqsCommand : public Command { private: string fastafile, outputDir; bool abort; - int end; + int end, fromend; + + string getChoppedAligned(Sequence); + string getChoppedUnaligned(Sequence); }; #endif diff --git a/classify.cpp b/classify.cpp index e07344d..7f45126 100644 --- a/classify.cpp +++ b/classify.cpp @@ -128,7 +128,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me gobble(fastaFile); names.push_back(temp.getName()); - + database->addSequence(temp); } fastaFile.close(); @@ -153,6 +153,11 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me #endif database->setNumSeqs(names.size()); + //sanity check + bool okay = phyloTree->ErrorCheck(names); + + if (!okay) { m->control_pressed = true; } + m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " seconds generate search database. "); m->mothurOutEndLine(); diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp index 1e4e42f..ab8bdcf 100644 --- a/clustersplitcommand.cpp +++ b/clustersplitcommand.cpp @@ -27,7 +27,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option) { else { //valid paramters for this command - string Array[] = {"phylip","column","name","cutoff","precision","method","showabund","timing","hard","processors","splitcutoff","outputdir","inputdir"}; + string Array[] = {"phylip","column","name","cutoff","precision","method","showabund","timing","hard","processors","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -121,11 +121,6 @@ ClusterSplitCommand::ClusterSplitCommand(string option) { convert(temp, cutoff); if (!hard) { cutoff += (5 / (precision * 10.0)); } - temp = validParameter.validFile(parameters, "splitcutoff", false); - if (temp == "not found") { temp = "0.10"; } - convert(temp, splitcutoff); - if (!hard) { splitcutoff += (5 / (precision * 10.0)); } - method = validParameter.validFile(parameters, "method", false); if (method == "not found") { method = "furthest"; } @@ -208,7 +203,7 @@ int ClusterSplitCommand::execute(){ time_t estart = time(NULL); //split matrix into non-overlapping groups - SplitMatrix* split = new SplitMatrix(distfile, namefile, splitcutoff); + SplitMatrix* split = new SplitMatrix(distfile, namefile, cutoff); split->split(); if (m->control_pressed) { delete split; return 0; } diff --git a/commandfactory.cpp b/commandfactory.cpp index 0bca8c0..4d2b0ae 100644 --- a/commandfactory.cpp +++ b/commandfactory.cpp @@ -164,7 +164,7 @@ CommandFactory::CommandFactory(){ commands["clearcut"] = "clearcut"; commands["catchall"] = "catchall"; commands["split.abund"] = "split.abund"; - commands["cluster.split"] = "cluster.split"; + //commands["cluster.split"] = "cluster.split"; commands["classify.seqs"] = "MPIEnabled"; commands["dist.seqs"] = "MPIEnabled"; commands["filter.seqs"] = "MPIEnabled"; @@ -287,7 +287,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){ else if(commandName == "clearcut") { command = new ClearcutCommand(optionString); } else if(commandName == "catchall") { command = new CatchAllCommand(optionString); } else if(commandName == "split.abund") { command = new SplitAbundCommand(optionString); } - else if(commandName == "cluster.split") { command = new ClusterSplitCommand(optionString); } + //else if(commandName == "cluster.split") { command = new ClusterSplitCommand(optionString); } else { command = new NoCommand(optionString); } return command; diff --git a/makefile b/makefile index 566c6b0..fdcef27 100644 --- a/makefile +++ b/makefile @@ -1,1701 +1,1701 @@ -################################################### -# -# 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 - -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\ - ./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\ - ./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\ - ./readcluster.o\ - ./ccode.o\ - ./taxonomyequalizer.o\ - ./phylotypecommand.o\ - ./classifyseqscommand.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\ - ./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\ - ./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\ - ./readcluster.o\ - ./ccode.o\ - ./taxonomyequalizer.o\ - ./phylotypecommand.o\ - ./classifyseqscommand.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 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\ - ./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\ - ./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\ - ./readcluster.o\ - ./ccode.o\ - ./taxonomyequalizer.o\ - ./phylotypecommand.o\ - ./classifyseqscommand.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 : splitabundcommand - $(CC) $(CC_OPTIONS) splitabundcommand -c $(INCLUDE) -o ./splitabundcommand - -# Item # 206 -- splitmatrix -- -./splitmatrix : splitmatrix - $(CC) $(CC_OPTIONS) splitmatrix -c $(INCLUDE) -o ./splitmatrix - -# Item # 207 -- splitmatrix -- -./clustersplitcommand : clustersplitcommand - $(CC) $(CC_OPTIONS) clustersplitcommand -c $(INCLUDE) -o ./clustersplitcommand - -##### END RUN #### +################################################### +# +# Makefile for mothur +# Creator [Xcode -> Makefile Ver: Feb 14 2007 09:18:41] +# Created: April 16, 2010 +# +################################################### + +# +# Macros +# + +CC = g++ +CC_OPTIONS = -O3 + +# if you do not want to use the readline library set to no, default yes. +# make sure you have the library installed + +USEREADLINE ?= yes + +ifeq ($(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\ + ./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\ + ./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\ + ./readcluster.o\ + ./ccode.o\ + ./taxonomyequalizer.o\ + ./phylotypecommand.o\ + ./classifyseqscommand.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\ + ./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\ + ./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\ + ./readcluster.o\ + ./ccode.o\ + ./taxonomyequalizer.o\ + ./phylotypecommand.o\ + ./classifyseqscommand.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\ + ./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\ + ./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\ + ./readcluster.o\ + ./ccode.o\ + ./taxonomyequalizer.o\ + ./phylotypecommand.o\ + ./classifyseqscommand.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.o + $(CC) $(CC_OPTIONS) splitmatrix.cpp -c $(INCLUDE) -o ./splitmatrix.o + +# Item # 207 -- splitmatrix -- +./clustersplitcommand.o : clustersplitcommand.cpp + $(CC) $(CC_OPTIONS) clustersplitcommand.cpp -c $(INCLUDE) -o ./clustersplitcommand.o + +##### END RUN #### diff --git a/mothur.cpp b/mothur.cpp index 43b838c..0249f65 100644 --- a/mothur.cpp +++ b/mothur.cpp @@ -73,9 +73,9 @@ int main(int argc, char *argv[]){ #endif //header - m->mothurOut("mothur v.1.10.0"); + m->mothurOut("mothur v.1.10.2"); m->mothurOutEndLine(); - m->mothurOut("Last updated: 5/14/2010"); + m->mothurOut("Last updated: 5/26/2010"); m->mothurOutEndLine(); m->mothurOutEndLine(); m->mothurOut("by"); diff --git a/phylotree.cpp b/phylotree.cpp index bfac59c..1c2deba 100644 --- a/phylotree.cpp +++ b/phylotree.cpp @@ -32,6 +32,8 @@ PhyloTree::PhyloTree(ifstream& in, string filename){ try { m = MothurOut::getInstance(); calcTotals = false; + numNodes = 0; + numSeqs = 0; #ifdef USE_MPI MPI_File inMPI; @@ -216,6 +218,7 @@ string PhyloTree::getNextTaxon(string& heirarchy){ int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){ try { + numSeqs++; map::iterator childPointer; @@ -236,6 +239,8 @@ int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){ //use print to reassign the taxa id taxon = getNextTaxon(seqTaxonomy); + if (taxon == "") { m->mothurOut(seqName + " has an error in the taxonomy. This may be due to a ;;"); m->mothurOutEndLine(); if (currentNode != 0) { uniqueTaxonomies[currentNode] = currentNode; } break; } + childPointer = tree[currentNode].children.find(taxon); if(childPointer != tree[currentNode].children.end()){ //if the node already exists, move on @@ -260,7 +265,7 @@ int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){ // tree[currentNode].childNumber = numChildren; // tree[currentNode].heirarchyID = heirarchyID + '.' + toString(tree[currentNode].childNumber); } - + if (seqTaxonomy == "") { uniqueTaxonomies[currentNode] = currentNode; } } @@ -520,7 +525,6 @@ void PhyloTree::printTreeNodes(string treefilename) { for (it2=uniqueTaxonomies.begin(); it2!=uniqueTaxonomies.end(); it2++) { outTree << it2->first << '\t' << tree[it2->first].accessions.size() << endl; } outTree << endl; - outTree.close(); #ifdef USE_MPI @@ -535,6 +539,93 @@ void PhyloTree::printTreeNodes(string treefilename) { } } /**************************************************************************************************/ +TaxNode PhyloTree::get(int i ){ + try { + if (i < tree.size()) { return tree[i]; } + else { cout << i << '\t' << tree.size() << endl ; m->mothurOut("Mismatch with taxonomy and template files. Cannot continue."); m->mothurOutEndLine(); exit(1); } + } + catch(exception& e) { + m->errorOut(e, "PhyloTree", "get"); + exit(1); + } +} +/**************************************************************************************************/ +TaxNode PhyloTree::get(string seqName){ + try { + map::iterator itFind = name2Taxonomy.find(seqName); + + if (itFind != name2Taxonomy.end()) { return tree[name2Taxonomy[seqName]]; } + else { m->mothurOut("Cannot find " + seqName + ". Mismatch with taxonomy and template files. Cannot continue."); m->mothurOutEndLine(); exit(1);} + } + catch(exception& e) { + m->errorOut(e, "PhyloTree", "get"); + exit(1); + } +} +/**************************************************************************************************/ +string PhyloTree::getName(int i ){ + try { + if (i < tree.size()) { return tree[i].name; } + else { m->mothurOut("Mismatch with taxonomy and template files. Cannot continue."); m->mothurOutEndLine(); exit(1); } + } + catch(exception& e) { + m->errorOut(e, "PhyloTree", "get"); + exit(1); + } +} +/**************************************************************************************************/ +int PhyloTree::getIndex(string seqName){ + try { + map::iterator itFind = name2Taxonomy.find(seqName); + + if (itFind != name2Taxonomy.end()) { return name2Taxonomy[seqName]; } + else { m->mothurOut("Cannot find " + seqName + ". Mismatch with taxonomy and template files. Cannot continue."); m->mothurOutEndLine(); exit(1);} + } + catch(exception& e) { + m->errorOut(e, "PhyloTree", "get"); + exit(1); + } +} +/**************************************************************************************************/ +bool PhyloTree::ErrorCheck(vector templateFileNames){ + try { + + bool okay = true; + + map::iterator itFind; + map taxonomyFileNames = name2Taxonomy; + + for (int i = 0; i < templateFileNames.size(); i++) { + itFind = taxonomyFileNames.find(templateFileNames[i]); + + if (itFind != name2Taxonomy.end()) { //found it so erase it + taxonomyFileNames.erase(itFind); + }else { + m->mothurOut(templateFileNames[i] + " is in your template file and is not in your taxonomy file. Please correct."); m->mothurOutEndLine(); + okay = false; + } + + templateFileNames.erase(templateFileNames.begin()+i); + i--; + } + + if (taxonomyFileNames.size() > 0) { //there are names in tax file that are not in template + okay = false; + + for (itFind = taxonomyFileNames.begin(); itFind != taxonomyFileNames.end(); itFind++) { + m->mothurOut(itFind->first + " is in your taxonomy file and is not in your template file. Please correct."); m->mothurOutEndLine(); + } + } + + return okay; + } + catch(exception& e) { + m->errorOut(e, "PhyloTree", "ErrorCheck"); + exit(1); + } +} +/**************************************************************************************************/ + diff --git a/phylotree.h b/phylotree.h index 2f37450..a961721 100644 --- a/phylotree.h +++ b/phylotree.h @@ -41,13 +41,15 @@ public: vector getGenusTotals(); void setUp(string); //used to create file needed for summary file if you use () constructor and add seqs manually instead of passing taxonomyfile - TaxNode get(int i) { return tree[i]; } - TaxNode get(string seqName) { return tree[name2Taxonomy[seqName]]; } - int getIndex(string seqName) { return name2Taxonomy[seqName]; } - string getName(int i) { return tree[i].name; } + TaxNode get(int i); + TaxNode get(string seqName); + string getName(int i); + int getIndex(string seqName); + string getFullTaxonomy(string); //pass a sequence name return taxonomy int getMaxLevel() { return maxLevel; } int getNumSeqs() { return numSeqs; } + bool ErrorCheck(vector); private: string getNextTaxon(string&); -- 2.39.5