X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffinfocommand.cpp;h=4e53f69cb3e7dd51c3d4b30c10a09d76339b6f2c;hb=8f7164a88df624fd0a8d1eddbb3d744463cc9ecb;hp=f8ba25b5fabd1b8485065a548e47911cb0c8c1e3;hpb=058715887611e00dc18324cb0bd4a4a8472530b3;p=mothur.git

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index f8ba25b..4e53f69 100644
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -405,7 +405,7 @@ int SffInfoCommand::readHeader(ifstream& in, Header& header){
 			char buffer4 [2];
 			in.read(buffer4, 2);
 			header.clipQualLeft =  be_int2(*(unsigned short *)(&buffer4));
-			header.clipQualLeft = 5;
+			header.clipQualLeft = 5; 
 			
 			//read clip qual right
 			char buffer5 [2];
@@ -562,6 +562,7 @@ int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read, Header& hea
 		for (int i = 0; i < read.flowIndex.size(); i++) {  sum +=  read.flowIndex[i];  out << sum << '\t'; }
 		
 		//make the bases you want to clip lowercase and the bases you want to keep upper case
+		if(header.clipQualRight == 0){	header.clipQualRight = read.bases.length();	}
 		for (int i = 0; i < (header.clipQualLeft-1); i++) { read.bases[i] = tolower(read.bases[i]); }
 		for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   read.bases[i] = toupper(read.bases[i]);  }
 		for (int i = (header.clipQualRight-1); i < read.bases.length(); i++) {   read.bases[i] = tolower(read.bases[i]);  }
@@ -586,7 +587,10 @@ int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& head
 		string seq = read.bases;
 		
 		if (trim) {
-			if(header.clipQualRight != 0){
+			if(header.clipQualRight < header.clipQualLeft){
+				seq = "NNNN";
+			}
+			else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
 				seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
 			}
 			else {
@@ -619,7 +623,10 @@ int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& heade
 	try {
 		
 		if (trim) {
-			if(header.clipQualRight != 0){
+			if(header.clipQualRight < header.clipQualLeft){
+				out << "0\t0\t0\t0";
+			}
+			else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
 				out << ">" << header.name << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
 				for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   out << read.qualScores[i] << '\t';	}
 			}