added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / parsefastaqcommand.cpp

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index 9509a20af2528392c2df8590aea61fef6a7665b4..06ea359e6740bd822691e9f8ab6e3e53454cc724 100644 (file)
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -33,8 +33,10 @@ string ParseFastaQCommand::getHelpString(){
        try {
                string helpString = "";
                helpString += "The fastq.info command reads a fastq file and creates a fasta and quality file.\n";
-               helpString += "The fastq.info command parameter is fastq, and it is required.\n";
+               helpString += "The fastq.info command parameters are fastq, fasta and qfile; fastq is required.\n";
                helpString += "The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n";
+        helpString += "The fasta parameter allows you to indicate whether you want a fasta file generated. Default=T.\n";
+        helpString += "The qfile parameter allows you to indicate whether you want a quality file generated. Default=T.\n";
                helpString += "Example fastq.info(fastaq=test.fastaq).\n";
                helpString += "Note: No spaces between parameter labels (i.e. fastq), '=' and yourFastQFile.\n";
                return helpString;
@@ -166,7 +168,7 @@ int ParseFastaQCommand::execute(){
                        
                        //sanity check sequence length and number of quality scores match
                        if (name2 != "") { if (name != name2) { m->mothurOut("[ERROR]: names do not match. read " + name + " for fasta and " + name2 + " for quality."); m->mothurOutEndLine(); m->control_pressed = true; break; } }
-                       if (quality.length() != sequence.length()) { m->mothurOut("[ERROR]: lengths do not match. read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; break; }
+                       if (quality.length() != sequence.length()) { m->mothurOut("[ERROR]: Lengths do not match for sequence " + name + ". Read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; break; }
                        
                        //print sequence info to files
                        if (fasta) { outFasta << ">" << name << endl << sequence << endl; }
@@ -214,7 +216,7 @@ vector<int> ParseFastaQCommand::convertQual(string qual) {
        try {
                vector<int> qualScores;
                
-               int controlChar = int('!');
+               int controlChar = int('@');
                
                for (int i = 0; i < qual.length(); i++) { 
                        int temp = int(qual[i]);