added end of file character to some type type reads. fixes while testing.

[mothur.git] / sffinfocommand.cpp

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index a1b7066482b973bcbaeebefdc718c5c96d70aae9..911009982a3ed7a3e5da2845094a82b1338b74a3 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -1039,7 +1039,11 @@ int SffInfoCommand::findGroup(Header header, seqRead read, int& barcode, int& pr
         
         if (trim) {
             if(header.clipQualRight < header.clipQualLeft){
-                seq = "NNNN";
+                if (header.clipQualRight == 0) { //don't trim right
+                    seq = seq.substr(header.clipQualLeft-1);
+                }else {
+                    seq = "NNNN";
+                }
             }
             else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
                 seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
@@ -1260,7 +1264,11 @@ int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& head
                
         if (trim) {
                        if(header.clipQualRight < header.clipQualLeft){
-                               seq = "NNNN";
+                               if (header.clipQualRight == 0) { //don't trim right
+                    seq = seq.substr(header.clipQualLeft-1);
+                }else {
+                    seq = "NNNN";
+                }
                        }
                        else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
                                seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
@@ -1296,8 +1304,13 @@ int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& heade
                
                if (trim) {
                        if(header.clipQualRight < header.clipQualLeft){
-                               out << ">" << header.name << " xy=" << header.xy << endl;
-                               out << "0\t0\t0\t0";
+                if (header.clipQualRight == 0) { //don't trim right
+                    out << ">" << header.name << " xy=" << header.xy << " length=" << (read.qualScores.size()-header.clipQualLeft) << endl;
+                    for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';      }       
+                }else {
+                    out << ">" << header.name << " xy=" << header.xy << endl;
+                    out << "0\t0\t0\t0";
+                }
                        }
                        else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
                                out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
@@ -1325,6 +1338,8 @@ int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& heade
 //**********************************************************************************************************************
 int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
        try {
+        if (header.clipQualRight == 0) { header.clipQualRight = read.flowgram.size(); }
+        
                if(header.clipQualRight > header.clipQualLeft){
                        
                        int rightIndex = 0;
@@ -1641,7 +1656,7 @@ bool SffInfoCommand::readOligos(string oligoFile){
                                        // get rest of line in case there is a primer name
                                        while (!inOligos.eof()) {       
                                                char c = inOligos.get(); 
-                                               if (c == 10 || c == 13){        break;  }
+                                               if (c == 10 || c == 13 || c == -1){     break;  }
                                                else if (c == 32 || c == 9){;} //space or tab
                                                else {  group += c;  }
                                        }