Revert to previous commit

[mothur.git] / chopseqscommand.cpp

diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index e2b0fa46fc28bb6fd6be1af8a085e409a9a8b4df..4e06201cd352104b5ee9c9d1c41764d16473003e 100644 (file)
--- a/chopseqscommand.cpp
+++ b/chopseqscommand.cpp
@@ -121,7 +121,7 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(fastafile);      }
                        
                        string temp = validParameter.validFile(parameters, "numbases", false);  if (temp == "not found") { temp = "0"; } 
-                       convert(temp, numbases);   
+                       m->mothurConvert(temp, numbases);   
                        
                        temp = validParameter.validFile(parameters, "countgaps", false);        if (temp == "not found") { temp = "f"; } 
                        countGaps = m->isTrue(temp);  
@@ -233,7 +233,7 @@ string ChopSeqsCommand::getChopped(Sequence seq) {
                                        
                                        for (int i = 0; i < temp.length(); i++) {
                                                //eliminate N's
-                                               if (toupper(temp[i]) == 'N') { temp[i] == '.'; }
+                                               if (toupper(temp[i]) == 'N') { temp[i] = '.'; }
                                                
                                                numBasesCounted++; 
                                                
@@ -241,7 +241,7 @@ string ChopSeqsCommand::getChopped(Sequence seq) {
                                        }
                                        
                                        if (stopSpot == 0) { temp = ""; }
-                                       else {  temp = temp.substr(0, stopSpot);  }
+                                       else {  temp = temp.substr(0, stopSpot+1);  }
                                                        
                                }else { 
                                        if (!Short) { temp = ""; } //sequence too short
@@ -255,7 +255,7 @@ string ChopSeqsCommand::getChopped(Sequence seq) {
                                        
                                        for (int i = (temp.length()-1); i >= 0; i--) {
                                                //eliminate N's
-                                               if (toupper(temp[i]) == 'N') { temp[i] == '.'; }
+                                               if (toupper(temp[i]) == 'N') { temp[i] = '.'; }
                                                
                                                numBasesCounted++; 
 
@@ -283,7 +283,7 @@ string ChopSeqsCommand::getChopped(Sequence seq) {
                                        for (int i = 0; i < temp.length(); i++) {
                                                //eliminate N's
                                                if (toupper(temp[i]) == 'N') { 
-                                                       temp[i] == '.'; 
+                                                       temp[i] = '.'; 
                                                        tempLength--;
                                                        if (tempLength < numbases) { stopSpot = 0; break; }
                                                }
@@ -294,7 +294,7 @@ string ChopSeqsCommand::getChopped(Sequence seq) {
                                        }
                                        
                                        if (stopSpot == 0) { temp = ""; }
-                                       else {  temp = temp.substr(0, stopSpot);  }
+                                       else {  temp = temp.substr(0, stopSpot+1);  }
                                                        
                                }else { 
                                        if (!Short) { temp = ""; } //sequence too short
@@ -309,7 +309,7 @@ string ChopSeqsCommand::getChopped(Sequence seq) {
                                        for (int i = (temp.length()-1); i >= 0; i--) {
                                                //eliminate N's
                                                if (toupper(temp[i]) == 'N') { 
-                                                       temp[i] == '.'; 
+                                                       temp[i] = '.'; 
                                                        tempLength--;
                                                        if (tempLength < numbases) { stopSpot = 0; break; }
                                                }
@@ -320,7 +320,7 @@ string ChopSeqsCommand::getChopped(Sequence seq) {
                                        }
                                
                                        if (stopSpot == 0) { temp = ""; }
-                                       else {  temp = temp.substr(stopSpot+1);  }
+                                       else {  temp = temp.substr(stopSpot);  }
                                }else { 
                                        if (!Short) { temp = ""; } //sequence too short
                                }