added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / chopseqscommand.cpp

diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index e2b0fa46fc28bb6fd6be1af8a085e409a9a8b4df..68576cdb521efc994bedf2d3b2d40cc98a740b9c 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);  
@@ -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
@@ -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
@@ -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
                                }