Skip to content

Commit

Permalink
Adds vsearch to cluster.split
Browse files Browse the repository at this point in the history 
Issue #169
  • Loading branch information
@mothur-westcott
mothur-westcott committed Nov 5, 2015
1 parent 4174b4f commit 0f33eda
Show file tree
Hide file tree
Showing 17 changed files with 367 additions and 222 deletions.
16 changes: 0 additions & 16 deletions Mothur.xcodeproj/project.pbxproj
View file
Expand Up @@ -165,7 +165,6 @@
481FB5C01AC1B74F0076CFF3 /* getlineagecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */; };
481FB5C11AC1B74F0076CFF3 /* getlistcountcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6FA12D37EC400DA6239 /* getlistcountcommand.cpp */; };
481FB5C21AC1B74F0076CFF3 /* getoturepcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6FE12D37EC400DA6239 /* getoturepcommand.cpp */; };
481FB5C31AC1B74F0076CFF3 /* getotuscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70012D37EC400DA6239 /* getotuscommand.cpp */; };
481FB5C41AC1B74F0076CFF3 /* getotulabelscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70056E5156A93D000924A2D /* getotulabelscommand.cpp */; };
481FB5C51AC1B74F0076CFF3 /* getrabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70212D37EC400DA6239 /* getrabundcommand.cpp */; };
481FB5C61AC1B74F0076CFF3 /* getrelabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70412D37EC400DA6239 /* getrelabundcommand.cpp */; };
Expand Down Expand Up @@ -221,7 +220,6 @@
481FB5F91AC1B77E0076CFF3 /* removedistscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7B0231416B8244B006BA09E /* removedistscommand.cpp */; };
481FB5FA1AC1B77E0076CFF3 /* removegroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */; };
481FB5FB1AC1B77E0076CFF3 /* removelineagecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */; };
481FB5FC1AC1B7970076CFF3 /* removeotuscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */; };
481FB5FD1AC1B7970076CFF3 /* removeotulabelscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70056EA156AB6E500924A2D /* removeotulabelscommand.cpp */; };
481FB5FE1AC1B7970076CFF3 /* removerarecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A727864312E9E28C00F86ABA /* removerarecommand.cpp */; };
481FB5FF1AC1B7970076CFF3 /* removeseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */; };
Expand Down Expand Up @@ -627,7 +625,6 @@
A7E9B8D112D37EC400DA6239 /* getlistcountcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6FA12D37EC400DA6239 /* getlistcountcommand.cpp */; };
A7E9B8D212D37EC400DA6239 /* getopt_long.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6FC12D37EC400DA6239 /* getopt_long.cpp */; };
A7E9B8D312D37EC400DA6239 /* getoturepcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6FE12D37EC400DA6239 /* getoturepcommand.cpp */; };
A7E9B8D412D37EC400DA6239 /* getotuscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70012D37EC400DA6239 /* getotuscommand.cpp */; };
A7E9B8D512D37EC400DA6239 /* getrabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70212D37EC400DA6239 /* getrabundcommand.cpp */; };
A7E9B8D612D37EC400DA6239 /* getrelabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70412D37EC400DA6239 /* getrelabundcommand.cpp */; };
A7E9B8D712D37EC400DA6239 /* getsabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70612D37EC400DA6239 /* getsabundcommand.cpp */; };
Expand Down Expand Up @@ -716,7 +713,6 @@
A7E9B93012D37EC400DA6239 /* readtree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7BF12D37EC400DA6239 /* readtree.cpp */; };
A7E9B93212D37EC400DA6239 /* removegroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */; };
A7E9B93312D37EC400DA6239 /* removelineagecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */; };
A7E9B93412D37EC400DA6239 /* removeotuscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */; };
A7E9B93512D37EC400DA6239 /* removeseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */; };
A7E9B93612D37EC400DA6239 /* reportfile.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7CB12D37EC400DA6239 /* reportfile.cpp */; };
A7E9B93712D37EC400DA6239 /* reversecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */; };
Expand Down Expand Up @@ -1322,8 +1318,6 @@
A7E9B6FD12D37EC400DA6239 /* getopt_long.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = getopt_long.h; path = source/clearcut/getopt_long.h; sourceTree = "<group>"; };
A7E9B6FE12D37EC400DA6239 /* getoturepcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = getoturepcommand.cpp; path = /Users/sarahwestcott/Desktop/mothur/source/commands/getoturepcommand.cpp; sourceTree = "<absolute>"; };
A7E9B6FF12D37EC400DA6239 /* getoturepcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = getoturepcommand.h; path = /Users/sarahwestcott/Desktop/mothur/source/commands/getoturepcommand.h; sourceTree = "<absolute>"; };
A7E9B70012D37EC400DA6239 /* getotuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = getotuscommand.cpp; path = /Users/sarahwestcott/Desktop/mothur/source/commands/getotuscommand.cpp; sourceTree = "<absolute>"; };
A7E9B70112D37EC400DA6239 /* getotuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = getotuscommand.h; path = /Users/sarahwestcott/Desktop/mothur/source/commands/getotuscommand.h; sourceTree = "<absolute>"; };
A7E9B70212D37EC400DA6239 /* getrabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; name = getrabundcommand.cpp; path = /Users/sarahwestcott/Desktop/mothur/source/commands/getrabundcommand.cpp; sourceTree = "<absolute>"; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
A7E9B70312D37EC400DA6239 /* getrabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = getrabundcommand.h; path = /Users/sarahwestcott/Desktop/mothur/source/commands/getrabundcommand.h; sourceTree = "<absolute>"; };
A7E9B70412D37EC400DA6239 /* getrelabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = getrelabundcommand.cpp; path = /Users/sarahwestcott/Desktop/mothur/source/commands/getrelabundcommand.cpp; sourceTree = "<absolute>"; };
Expand Down Expand Up @@ -1507,8 +1501,6 @@
A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = removegroupscommand.h; path = /Users/sarahwestcott/Desktop/mothur/source/commands/removegroupscommand.h; sourceTree = "<absolute>"; };
A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = removelineagecommand.cpp; path = /Users/sarahwestcott/Desktop/mothur/source/commands/removelineagecommand.cpp; sourceTree = "<absolute>"; };
A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = removelineagecommand.h; path = /Users/sarahwestcott/Desktop/mothur/source/commands/removelineagecommand.h; sourceTree = "<absolute>"; };
A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = removeotuscommand.cpp; path = /Users/sarahwestcott/Desktop/mothur/source/commands/removeotuscommand.cpp; sourceTree = "<absolute>"; };
A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = removeotuscommand.h; path = /Users/sarahwestcott/Desktop/mothur/source/commands/removeotuscommand.h; sourceTree = "<absolute>"; };
A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = removeseqscommand.cpp; path = /Users/sarahwestcott/Desktop/mothur/source/commands/removeseqscommand.cpp; sourceTree = "<absolute>"; };
A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = removeseqscommand.h; path = /Users/sarahwestcott/Desktop/mothur/source/commands/removeseqscommand.h; sourceTree = "<absolute>"; };
A7E9B7CB12D37EC400DA6239 /* reportfile.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = reportfile.cpp; path = source/datastructures/reportfile.cpp; sourceTree = "<group>"; };
Expand Down Expand Up @@ -2163,8 +2155,6 @@
A7E9B6FA12D37EC400DA6239 /* getlistcountcommand.cpp */,
A7E9B6FF12D37EC400DA6239 /* getoturepcommand.h */,
A7E9B6FE12D37EC400DA6239 /* getoturepcommand.cpp */,
A7E9B70112D37EC400DA6239 /* getotuscommand.h */,
A7E9B70012D37EC400DA6239 /* getotuscommand.cpp */,
A70056E8156A93E300924A2D /* getotulabelscommand.h */,
A70056E5156A93D000924A2D /* getotulabelscommand.cpp */,
A7E9B70312D37EC400DA6239 /* getrabundcommand.h */,
Expand Down Expand Up @@ -2279,8 +2269,6 @@
A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */,
A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */,
A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */,
A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */,
A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */,
A70056E9156AB6D400924A2D /* removeotulabelscommand.h */,
A70056EA156AB6E500924A2D /* removeotulabelscommand.cpp */,
A727864212E9E28C00F86ABA /* removerarecommand.h */,
Expand Down Expand Up @@ -2872,7 +2860,6 @@
481FB58C1AC1B6FF0076CFF3 /* slayer.cpp in Sources */,
481FB6531AC1B8100076CFF3 /* gotohoverlap.cpp in Sources */,
481FB66D1AC1B8520076CFF3 /* rftreenode.cpp in Sources */,
481FB5C31AC1B74F0076CFF3 /* getotuscommand.cpp in Sources */,
481FB65B1AC1B82C0076CFF3 /* mothurfisher.cpp in Sources */,
481FB6721AC1B8820076CFF3 /* refchimeratest.cpp in Sources */,
481FB6051AC1B7970076CFF3 /* seqerrorcommand.cpp in Sources */,
Expand Down Expand Up @@ -3178,7 +3165,6 @@
481FB5A21AC1B71B0076CFF3 /* clearcutcommand.cpp in Sources */,
481FB5851AC1B6FF0076CFF3 /* chimeracheckrdp.cpp in Sources */,
481FB55C1AC1B6660076CFF3 /* sharedbraycurtis.cpp in Sources */,
481FB5FC1AC1B7970076CFF3 /* removeotuscommand.cpp in Sources */,
481FB5BE1AC1B74F0076CFF3 /* getmetacommunitycommand.cpp in Sources */,
481FB6821AC1B8AF0076CFF3 /* svm.cpp in Sources */,
481FB6911AC1BAA60076CFF3 /* phylotree.cpp in Sources */,
Expand Down Expand Up @@ -3325,7 +3311,6 @@
A7E9B8D112D37EC400DA6239 /* getlistcountcommand.cpp in Sources */,
A7E9B8D212D37EC400DA6239 /* getopt_long.cpp in Sources */,
A7E9B8D312D37EC400DA6239 /* getoturepcommand.cpp in Sources */,
A7E9B8D412D37EC400DA6239 /* getotuscommand.cpp in Sources */,
A7E9B8D512D37EC400DA6239 /* getrabundcommand.cpp in Sources */,
A7E9B8D612D37EC400DA6239 /* getrelabundcommand.cpp in Sources */,
A7E9B8D712D37EC400DA6239 /* getsabundcommand.cpp in Sources */,
Expand Down Expand Up @@ -3429,7 +3414,6 @@
A7E9B93012D37EC400DA6239 /* readtree.cpp in Sources */,
A7E9B93212D37EC400DA6239 /* removegroupscommand.cpp in Sources */,
A7E9B93312D37EC400DA6239 /* removelineagecommand.cpp in Sources */,
A7E9B93412D37EC400DA6239 /* removeotuscommand.cpp in Sources */,
A7E9B93512D37EC400DA6239 /* removeseqscommand.cpp in Sources */,
48A52FDE1BC428DF00548F6C /* util.cc in Sources */,
A7E9B93612D37EC400DA6239 /* reportfile.cpp in Sources */,
Expand Down
4 changes: 2 additions & 2 deletions makefile-internal
View file
Expand Up @@ -10,7 +10,7 @@ VERSION = "\"1.36.1\""

ifeq ($(strip $(64BIT_VERSION)),yes)
#if you are a mac user use the following line
TARGET_ARCH += -arch x86_64
#TARGET_ARCH += -arch x86_64

#if you using cygwin to build Windows the following line
#CXX = x86_64-w64-mingw32-g++
Expand Down Expand Up @@ -95,4 +95,4 @@ install : mothur

clean :
@rm -f $(OBJECTS)
@rm -f uchime
@rm -f uchime
27 changes: 10 additions & 17 deletions source/commandfactory.cpp
View file
Expand Up @@ -93,8 +93,6 @@
#include "subsamplecommand.h"
#include "removegroupscommand.h"
#include "getgroupscommand.h"
#include "getotuscommand.h"
#include "removeotuscommand.h"
#include "indicatorcommand.h"
#include "consensusseqscommand.h"
#include "trimflowscommand.h"
Expand Down Expand Up @@ -303,6 +301,7 @@ CommandFactory::CommandFactory(){
commands["create.database"] = "create.database";
commands["make.biom"] = "make.biom";
commands["get.coremicrobiome"] = "get.coremicrobiome";
commands["list.otus"] = "list.otus";
commands["list.otulabels"] = "list.otulabels";
commands["get.otulabels"] = "get.otulabels";
commands["remove.otulabels"] = "remove.otulabels";
Expand Down Expand Up @@ -518,8 +517,9 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
else if(commandName == "remove.lineage") { command = new RemoveLineageCommand(optionString); }
else if(commandName == "get.groups") { command = new GetGroupsCommand(optionString); }
else if(commandName == "remove.groups") { command = new RemoveGroupsCommand(optionString); }
else if(commandName == "get.otus") { command = new GetOtusCommand(optionString); }
else if(commandName == "remove.otus") { command = new RemoveOtusCommand(optionString); }
else if((commandName == "get.otus") || (commandName == "get.otulabels")) { command = new GetOtuLabelsCommand(optionString); }
else if((commandName == "remove.otus") || (commandName == "remove.otulabels")) { command = new RemoveOtuLabelsCommand(optionString); }
else if((commandName == "list.otus") ||(commandName == "list.otulabels")) { command = new ListOtuLabelsCommand(optionString); }
else if(commandName == "fastq.info") { command = new ParseFastaQCommand(optionString); }
else if(commandName == "pipeline.pds") { command = new PipelineCommand(optionString); }
else if(commandName == "deunique.seqs") { command = new DeUniqueSeqsCommand(optionString); }
Expand Down Expand Up @@ -556,9 +556,6 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
else if(commandName == "create.database") { command = new CreateDatabaseCommand(optionString); }
else if(commandName == "make.biom") { command = new MakeBiomCommand(optionString); }
else if(commandName == "get.coremicrobiome") { command = new GetCoreMicroBiomeCommand(optionString); }
else if(commandName == "list.otulabels") { command = new ListOtuLabelsCommand(optionString); }
else if(commandName == "get.otulabels") { command = new GetOtuLabelsCommand(optionString); }
else if(commandName == "remove.otulabels") { command = new RemoveOtuLabelsCommand(optionString); }
else if(commandName == "make.contigs") { command = new MakeContigsCommand(optionString); }
else if(commandName == "load.logfile") { command = new LoadLogfileCommand(optionString); }
else if(commandName == "sff.multiple") { command = new SffMultipleCommand(optionString); }
Expand Down Expand Up @@ -695,8 +692,9 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
else if(commandName == "get.groups") { pipecommand = new GetGroupsCommand(optionString); }
else if(commandName == "remove.lineage") { pipecommand = new RemoveLineageCommand(optionString); }
else if(commandName == "remove.groups") { pipecommand = new RemoveGroupsCommand(optionString); }
else if(commandName == "get.otus") { pipecommand = new GetOtusCommand(optionString); }
else if(commandName == "remove.otus") { pipecommand = new RemoveOtusCommand(optionString); }
else if((commandName == "get.otus") || (commandName == "get.otulabels")) { pipecommand = new GetOtuLabelsCommand(optionString); }
else if((commandName == "remove.otus") || (commandName == "remove.otulabels")) { pipecommand = new RemoveOtuLabelsCommand(optionString); }
else if((commandName == "list.otus") ||(commandName == "list.otulabels")) { pipecommand = new ListOtuLabelsCommand(optionString); }
else if(commandName == "fastq.info") { pipecommand = new ParseFastaQCommand(optionString); }
else if(commandName == "deunique.seqs") { pipecommand = new DeUniqueSeqsCommand(optionString); }
else if(commandName == "pairwise.seqs") { pipecommand = new PairwiseSeqsCommand(optionString); }
Expand Down Expand Up @@ -732,9 +730,6 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
else if(commandName == "create.database") { pipecommand = new CreateDatabaseCommand(optionString); }
else if(commandName == "make.biom") { pipecommand = new MakeBiomCommand(optionString); }
else if(commandName == "get.coremicrobiome") { pipecommand = new GetCoreMicroBiomeCommand(optionString); }
else if(commandName == "list.otulabels") { pipecommand = new ListOtuLabelsCommand(optionString); }
else if(commandName == "get.otulabels") { pipecommand = new GetOtuLabelsCommand(optionString); }
else if(commandName == "remove.otulabels") { pipecommand = new RemoveOtuLabelsCommand(optionString); }
else if(commandName == "make.contigs") { pipecommand = new MakeContigsCommand(optionString); }
else if(commandName == "load.logfile") { pipecommand = new LoadLogfileCommand(optionString); }
else if(commandName == "sff.multiple") { pipecommand = new SffMultipleCommand(optionString); }
Expand Down Expand Up @@ -857,8 +852,9 @@ Command* CommandFactory::getCommand(string commandName){
else if(commandName == "remove.lineage") { shellcommand = new RemoveLineageCommand(); }
else if(commandName == "get.groups") { shellcommand = new GetGroupsCommand(); }
else if(commandName == "remove.groups") { shellcommand = new RemoveGroupsCommand(); }
else if(commandName == "get.otus") { shellcommand = new GetOtusCommand(); }
else if(commandName == "remove.otus") { shellcommand = new RemoveOtusCommand(); }
else if((commandName == "get.otus") || (commandName == "get.otulabels")) { shellcommand = new GetOtuLabelsCommand(); }
else if((commandName == "remove.otus") || (commandName == "remove.otulabels")) { shellcommand = new RemoveOtuLabelsCommand(); }
else if((commandName == "list.otus") ||(commandName == "list.otulabels")) { shellcommand = new ListOtuLabelsCommand(); }
else if(commandName == "fastq.info") { shellcommand = new ParseFastaQCommand(); }
else if(commandName == "deunique.seqs") { shellcommand = new DeUniqueSeqsCommand(); }
else if(commandName == "pairwise.seqs") { shellcommand = new PairwiseSeqsCommand(); }
Expand Down Expand Up @@ -894,9 +890,6 @@ Command* CommandFactory::getCommand(string commandName){
else if(commandName == "create.database") { shellcommand = new CreateDatabaseCommand(); }
else if(commandName == "make.biom") { shellcommand = new MakeBiomCommand(); }
else if(commandName == "get.coremicrobiome") { shellcommand = new GetCoreMicroBiomeCommand(); }
else if(commandName == "list.otulabels") { shellcommand = new ListOtuLabelsCommand(); }
else if(commandName == "get.otulabels") { shellcommand = new GetOtuLabelsCommand(); }
else if(commandName == "remove.otulabels") { shellcommand = new RemoveOtuLabelsCommand(); }
else if(commandName == "make.contigs") { shellcommand = new MakeContigsCommand(); }
else if(commandName == "load.logfile") { shellcommand = new LoadLogfileCommand(); }
else if(commandName == "sff.multiple") { shellcommand = new SffMultipleCommand(); }
Expand Down

0 comments on commit 0f33eda

Please sign in to comment.