From: pschloss <pschloss>
Date: Thu, 29 Jul 2010 06:05:49 +0000 (+0000)
Subject: another pds fix to sffinfo
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=2431fce75705f16d6d7cab7a6f5fe02051d82ca5

another pds fix to sffinfo
---

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index cb5f874..bbfcfd4 100644
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -410,6 +410,7 @@ int SffInfoCommand::readHeader(ifstream& in, Header& header){
 			char buffer5 [2];
 			in.read(buffer5, 2);
 			header.clipQualRight =  be_int2(*(unsigned short *)(&buffer5));
+			if(header.clipQualRight == 0){	header.clipQualRight = numBases;	}
 			
 			//read clipAdapterLeft
 			char buffer6 [2];
@@ -585,22 +586,14 @@ int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& head
 		string seq = read.bases;
 		
 		if (trim) {
-			if(header.clipQualRight != 0){
-				seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft+1));
-			}
-			else{
-				seq = seq.substr(header.clipQualLeft-1);
-			}
+			seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-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]);  }
-				
-				if(header.clipQualRight != 0){
-					for (int i = (header.clipQualRight-1); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }
-				}
+				for (int i = (header.clipQualRight-1); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }
 			}
 		}