added template=self capability to chimers.slayer, worked on corr.axes and added accno...

[mothur.git] / parsefastaqcommand.cpp

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index 31de119591dc333cc71ff08305822c018af861be..f0a7abcc3692b8e290863a71c93bcc1831e87fca 100644 (file)
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -25,6 +25,7 @@ vector<string> ParseFastaQCommand::getValidParameters(){
 //**********************************************************************************************************************
 ParseFastaQCommand::ParseFastaQCommand(){      
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
@@ -119,7 +120,7 @@ ParseFastaQCommand::ParseFastaQCommand(string option){
 
 void ParseFastaQCommand::help(){
        try {
-               m->mothurOut("The fastq.info command reads a fastaQ file and creates a fasta and quality file.\n");
+               m->mothurOut("The fastq.info command reads a fastq file and creates a fasta and quality file.\n");
                m->mothurOut("The fastq.info command parameter is fastq, and it is required.\n");
                m->mothurOut("The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n");
                m->mothurOut("Example fastq.info(fastaq=test.fastaq).\n");
@@ -174,7 +175,7 @@ int ParseFastaQCommand::execute(){
                        if (qual == "") {  m->mothurOut("[ERROR]: missing quality for " + name2); m->mothurOutEndLine(); m->control_pressed = true; break; }
                        
                        //sanity check sequence length and number of quality scores match
-                       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 (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 (qual.length() != sequence.length()) { m->mothurOut("[ERROR]: lengths do not match. read " + toString(sequence.length()) + " characters for fasta and " + toString(qual.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; break; }
                        
                        //convert quality scores