fixed bugs with trim.seqs and bdiffs

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index d4625478f17442e3bea270a80df246df2193baa8..6e97c882128e5579df63dacbc915dcda9c66c2e9 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -13,14 +13,8 @@
                A72B3A63118B37FD004B9F8D /* phylodiversitycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversitycommand.cpp; sourceTree = "<group>"; };
                A72B3A7B118B4D1B004B9F8D /* phylodiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversity.h; sourceTree = "<group>"; };
                A72B3A7C118B4D1B004B9F8D /* phylodiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversity.cpp; sourceTree = "<group>"; };
-               A730977D11A417BE00117C95 /* splitmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = splitmatrix.h; sourceTree = SOURCE_ROOT; };
-               A730977E11A417BE00117C95 /* splitmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = splitmatrix.cpp; sourceTree = SOURCE_ROOT; };
-               A73097B911A43E1300117C95 /* clustersplitcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clustersplitcommand.h; sourceTree = "<group>"; };
-               A73097BA11A43E1300117C95 /* clustersplitcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clustersplitcommand.cpp; sourceTree = "<group>"; };
                A73953DA11987ED100B0B160 /* chopseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chopseqscommand.h; sourceTree = "<group>"; };
                A73953DB11987ED100B0B160 /* chopseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chopseqscommand.cpp; sourceTree = "<group>"; };
-               A73F163411A1951D0087CA57 /* splitabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = splitabundcommand.h; sourceTree = "<group>"; };
-               A73F163511A1951D0087CA57 /* splitabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = splitabundcommand.cpp; sourceTree = "<group>"; };
                A747E79B1163442A00FB9042 /* chimeracheckcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeracheckcommand.h; sourceTree = "<group>"; };
                A747E79C1163442A00FB9042 /* chimeracheckcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeracheckcommand.cpp; sourceTree = "<group>"; };
                A747E81C116365E000FB9042 /* chimeraslayercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraslayercommand.h; sourceTree = "<group>"; };
@@ -674,10 +668,8 @@
                                A7DA201D113FECD400BF472F /* classifyseqscommand.cpp */,
                                A7D215C811996C6E00F13F13 /* clearcutcommand.h */,
                                A7D215C911996C6E00F13F13 /* clearcutcommand.cpp */,
-                               A7DA2022113FECD400BF472F /* clustercommand.h */,
                                A7DA2021113FECD400BF472F /* clustercommand.cpp */,
-                               A73097B911A43E1300117C95 /* clustersplitcommand.h */,
-                               A73097BA11A43E1300117C95 /* clustersplitcommand.cpp */,
+                               A7DA2022113FECD400BF472F /* clustercommand.h */,
                                A7DA2025113FECD400BF472F /* collectcommand.cpp */,
                                A7DA2026113FECD400BF472F /* collectcommand.h */,
                                A7DA2029113FECD400BF472F /* collectsharedcommand.cpp */,
@@ -772,8 +764,6 @@
                                A76C4A1111876BAF0009460B /* setlogfilecommand.cpp */,
                                A7DA2110113FECD400BF472F /* sharedcommand.h */,
                                A7DA210F113FECD400BF472F /* sharedcommand.cpp */,
-                               A73F163411A1951D0087CA57 /* splitabundcommand.h */,
-                               A73F163511A1951D0087CA57 /* splitabundcommand.cpp */,
                                A7DA2155113FECD400BF472F /* summarycommand.h */,
                                A7DA2154113FECD400BF472F /* summarycommand.cpp */,
                                A7DA2159113FECD400BF472F /* summarysharedcommand.h */,
@@ -925,8 +915,6 @@
                                A7DA20ED113FECD400BF472F /* readphylip.h */,
                                A7DA20EE113FECD400BF472F /* readtree.cpp */,
                                A7DA20EF113FECD400BF472F /* readtree.h */,
-                               A730977D11A417BE00117C95 /* splitmatrix.h */,
-                               A730977E11A417BE00117C95 /* splitmatrix.cpp */,
                        );
                        name = read;
                        sourceTree = "<group>";
@@ -991,7 +979,7 @@
                                GCC_WARN_UNUSED_VARIABLE = YES;
                                LINK_WITH_STANDARD_LIBRARIES = YES;
                                PREBINDING = NO;
-                               SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
+                               SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.6.sdk";
                        };
                        name = Release;
                };

diff --git a/makefile b/makefile
index f4af8e9b02a92cc0c9bf1d282ec5cacf9d0514f8..566c6b0381a3549778d6209d9579d67a5232df0d 100644 (file)
--- a/makefile
+++ b/makefile
@@ -26,7 +26,7 @@ ifeq  ($(strip $(USEREADLINE)),yes)
       -L../readline-6.0
 endif
 
-USEMPI ?= yes
+USEMPI ?= no
 
 ifeq  ($(strip $(USEMPI)),yes)
        CC = mpic++
@@ -459,7 +459,7 @@ mothur : \
                ./logsd.o\
                ./geom.o\
                ./setlogfilecommand.o\
-               -o ../Release/mothur
+               -o mothur
 
 clean : 
                rm \

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index ae9c436440950cca6cd33eb99e85c5b9b4db1062..5f7c9b2199d28960fe1b619a4df2394be3b352a6 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -364,7 +364,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                return 0;
                        }
                        
-                       bool success = 1;
+                       int success = 1;
                        
                        Sequence currSeq(inFASTA);
 
@@ -385,7 +385,6 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                        
                                if(barcodes.size() != 0){
                                        success = stripBarcode(currSeq, group);
-//                                     cout << "here: " << success << endl;
                                        if(success > bdiffs){   trashCode += 'b';       }
                                        else{ currentSeqsDiffs += success;  }
                                }
@@ -419,7 +418,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                if(flip){       currSeq.reverseComplement();    }               // should go last                       
                                
                                if(trashCode.length() == 0){
-                                       currSeq.setAligned(currSeq.getUnaligned());  //this is because of a modification we made to the sequence class to fix a bug.  all seqs have an aligned version, which is the version that gets printed.
+                                       currSeq.setAligned(currSeq.getUnaligned());
                                        currSeq.printSequence(outFASTA);
                                        if(barcodes.size() != 0){
                                                outGroups << currSeq.getName() << '\t' << groupVector[group] << endl;
@@ -432,6 +431,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                else{
                                        currSeq.setName(currSeq.getName() + '|' + trashCode);
                                        currSeq.setUnaligned(origSeq);
+                                       currSeq.setAligned(origSeq);
                                        currSeq.printSequence(scrapFASTA);
                                }
                        }
@@ -610,15 +610,16 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec){ //vector<ofstream*
 
 int TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
        try {
+               
                string rawSequence = seq.getUnaligned();
-               bool success = bdiffs + 1;      //guilty until proven innocent
+               int success = bdiffs + 1;       //guilty until proven innocent
                
                //can you find the barcode
                for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
                        string oligo = it->first;
                        if(rawSequence.length() < oligo.length()){      //let's just assume that the barcodes are the same length
-                               success = bdiffs + 1;
-                               break;
+                               success = bdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
+                               break;  
                        }
                        
                        if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
@@ -662,7 +663,7 @@ int TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
 //                             int length = oligo.length();
                                
                                if(rawSequence.length() < maxLength){   //let's just assume that the barcodes are the same length
-                                       success = bdiffs + 1;
+                                       success = bdiffs + 10;
                                        break;
                                }
                                
@@ -678,7 +679,6 @@ int TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
                                }
                                oligo = oligo.substr(0,alnLength);
                                temp = temp.substr(0,alnLength);
-//                             
                                
                                int newStart=0;
                                int numDiff = countDiffs(oligo, temp);
@@ -698,17 +698,20 @@ int TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
                                }
 
                        }
-                       if(minDiff > bdiffs){   success =  bdiffs + 1;  }
-                       else if(minCount > 1)   {       success =  bdiffs + 1;  }
-                       else{
+
+                       if(minDiff > bdiffs)    {       success = minDiff;              }       //no good matches
+                       else if(minCount > 1)   {       success = bdiffs + 100; }       //can't tell the difference between multiple barcodes
+                       else{                                                                                                   //use the best match
                                group = minGroup;
-                               seq.setUnaligned("*" + rawSequence.substr(minPos));
+                               seq.setUnaligned(rawSequence.substr(minPos));
                                success = minDiff;
                        }
                        
                        if (alignment != NULL) {  delete alignment;  }
                        
                }
+//             cout << success << endl;
+               
                return success;
                
        }
@@ -724,7 +727,7 @@ int TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
 int TrimSeqsCommand::stripForward(Sequence& seq){
        try {
                string rawSequence = seq.getUnaligned();
-               bool success = pdiffs + 1;      //guilty until proven innocent
+               int success = pdiffs + 1;       //guilty until proven innocent
                
                //can you find the primer
                for(int i=0;i<numFPrimers;i++){
@@ -772,7 +775,7 @@ int TrimSeqsCommand::stripForward(Sequence& seq){
                                string oligo = forPrimer[i];
                                
                                if(rawSequence.length() < maxLength){   
-                                       success = pdiffs + 1;
+                                       success = pdiffs + 100;
                                        break;
                                }
                                
@@ -788,7 +791,7 @@ int TrimSeqsCommand::stripForward(Sequence& seq){
                                }
                                oligo = oligo.substr(0,alnLength);
                                temp = temp.substr(0,alnLength);
-//                                                             
+
                                int newStart=0;
                                int numDiff = countDiffs(oligo, temp);
                                if(numDiff < minDiff){
@@ -806,10 +809,10 @@ int TrimSeqsCommand::stripForward(Sequence& seq){
                                }
 
                        }
-                       if(minDiff > pdiffs){   success =  pdiffs + 1;  }
-                       else if(minCount > 1)   {       success =  pdiffs + 1;  }
+                       if(minDiff > pdiffs)    {       success =  minDiff;             }
+                       else if(minCount > 1)   {       success =  pdiffs + 10; }
                        else{
-                               seq.setUnaligned("*" + rawSequence.substr(minPos));
+                               seq.setUnaligned(rawSequence.substr(minPos));
                                success = minDiff;
                        }