added dups parameter to chimera.uchime. working on make.contigs command.

[mothur.git] / removeseqscommand.cpp

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index 73873f3a4744eb0e9ce59a9b2640bf013f524852..00b94a9dac842ceeca4a2a0362d87f14ba12ca1b 100644 (file)
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -406,6 +406,12 @@ int RemoveSeqsCommand::readFasta(){
                        if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
                        
                        Sequence currSeq(in);
+            
+            if (!dups) {//adjust name if needed
+                map<string, string>::iterator it = uniqueMap.find(currSeq.getName());
+                if (it != uniqueMap.end()) { currSeq.setName(it->second); }
+            }
+
                        name = currSeq.getName();
                        
                        if (name != "") {
@@ -413,7 +419,7 @@ int RemoveSeqsCommand::readFasta(){
                                if (names.count(name) == 0) {
                                        wroteSomething = true;
                                        
-                                       currSeq.printSequence(out);
+                    currSeq.printSequence(out);
                                }else {  removedCount++;  }
                        }
                        m->gobble(in);
@@ -477,6 +483,11 @@ int RemoveSeqsCommand::readQual(){
                        
                        m->gobble(in);
                        
+            if (!dups) {//adjust name if needed
+                map<string, string>::iterator it = uniqueMap.find(saveName);
+                if (it != uniqueMap.end()) { name = ">" + it->second; saveName = it->second; }
+            }
+            
                        if (names.count(saveName) == 0) {
                                wroteSomething = true;
                                
@@ -695,6 +706,8 @@ int RemoveSeqsCommand::readName(){
                                                wroteSomething = true;
                                                
                                                out << validSecond[0] << '\t';
+                        //we are changing the unique name in the fasta file
+                        uniqueMap[firstCol] = validSecond[0];
                                                
                                                //you know you have at least one valid second since first column is valid
                                                for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
@@ -788,9 +801,15 @@ int RemoveSeqsCommand::readTax(){
                        in >> name;                             //read from first column
                        in >> tax;                      //read from second column
                        
+            if (!dups) {//adjust name if needed
+                map<string, string>::iterator it = uniqueMap.find(name);
+                if (it != uniqueMap.end()) { name = it->second; }
+            }
+            
                        //if this name is in the accnos file
                        if (names.count(name) == 0) {
                                wroteSomething = true;
+            
                                out << name << '\t' << tax << endl;
                        }else {  removedCount++;  }
                                        
@@ -840,6 +859,11 @@ int RemoveSeqsCommand::readAlign(){
                        if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
                        
                        in >> name;                             //read from first column
+            
+            if (!dups) {//adjust name if needed
+                map<string, string>::iterator it = uniqueMap.find(name);
+                if (it != uniqueMap.end()) { name = it->second; }
+            }
                        
                        //if this name is in the accnos file
                        if (names.count(name) == 0) {