X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chopseqscommand.cpp;h=68576cdb521efc994bedf2d3b2d40cc98a740b9c;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=e2b0fa46fc28bb6fd6be1af8a085e409a9a8b4df;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index e2b0fa4..68576cd 100644
--- 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
 				}