From: pschloss <pschloss>
Date: Thu, 29 Jul 2010 04:01:58 +0000 (+0000)
Subject: pds' small change to sffinfo
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=a3d9877d9c62058dbe167ceca159f4b76744f1cf

pds' small change to sffinfo
---

diff --git a/makefile b/makefile
index dccd2c3..55039af 100644
--- a/makefile
+++ b/makefile
@@ -48,7 +48,7 @@ ifeq  ($(strip $(USEREADLINE)),yes)
       -lncurses
 endif
 
-USEMPI ?= yes
+USEMPI ?= no
 
 ifeq  ($(strip $(USEMPI)),yes)
     CXX = mpic++
diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 8c0e473..cb5f874 100644
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -584,16 +584,23 @@ int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& head
 		
 		string seq = read.bases;
 		
-		
 		if (trim) {
-			seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft+1));
+			if(header.clipQualRight != 0){
+				seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft+1));
+			}
+			else{
+				seq = seq.substr(header.clipQualLeft-1);
+			}
 		}else{
 			//if you wanted the sfftxt then you already converted the bases to the right case
 			if (!sfftxt) {
 				//make the bases you want to clip lowercase and the bases you want to keep upper case
 				for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]);  }
 				for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++)  {   seq[i] = toupper(seq[i]);  }
-				for (int i = (header.clipQualRight-1); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }
+				
+				if(header.clipQualRight != 0){
+					for (int i = (header.clipQualRight-1); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }
+				}
 			}
 		}