added groups option to read.otu, added qtrim option to trim.seqs, fixed bug in get...

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 455cdc29aa47ecb1ca26a7f9b4021bef151d6314..5ca70a99cb4b600780b425ff7f29b909794cc362 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -21,7 +21,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string AlignArray[] =  {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile", "qthreshold", "qaverage", "allfiles"};
+                       string AlignArray[] =  {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile", "qthreshold", "qaverage", "allfiles", "qtrim"};
                        
                        vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
                        
@@ -72,6 +72,9 @@ TrimSeqsCommand::TrimSeqsCommand(string option){
                        
                        temp = validParameter.validFile(parameters, "qthreshold", false);       if (temp == "not found") { temp = "0"; }
                        convert(temp, qThreshold);
+                       
+                       temp = validParameter.validFile(parameters, "qtrim", false);    if (temp == "not found") { temp = "F"; }
+                       qtrim = isTrue(temp);
 
                        temp = validParameter.validFile(parameters, "qaverage", false);         if (temp == "not found") { temp = "0"; }
                        convert(temp, qAverage);
@@ -104,7 +107,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option){
 void TrimSeqsCommand::help(){
        try {
                mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
-               mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength and maxlength.\n");
+               mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, qtrim and allfiles.\n");
                mothurOut("The fasta parameter is required.\n");
                mothurOut("The flip parameter .... The default is 0.\n");
                mothurOut("The oligos parameter .... The default is "".\n");
@@ -112,11 +115,17 @@ void TrimSeqsCommand::help(){
                mothurOut("The maxhomop parameter .... The default is 0.\n");
                mothurOut("The minlength parameter .... The default is 0.\n");
                mothurOut("The maxlength parameter .... The default is 0.\n");
+               mothurOut("The qfile parameter .....\n");
+               mothurOut("The qthreshold parameter .... The default is 0.\n");
+               mothurOut("The qaverage parameter .... The default is 0.\n");
+               mothurOut("The allfiles parameter .... The default is F.\n");
+               mothurOut("The qtrim parameter .... The default is F.\n");
                mothurOut("The trim.seqs command should be in the following format: \n");
                mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig,  \n");
                mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n");       
                mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
-               mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+               mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
+               mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n\n");
 
        }
        catch(exception& e) {
@@ -170,6 +179,9 @@ int TrimSeqsCommand::execute(){
                        if(qFileName != ""){
                                if(qThreshold != 0)             {       success = stripQualThreshold(currSeq, qFile);   }
                                else if(qAverage != 0)  {       success = cullQualAverage(currSeq, qFile);              }
+                               if ((!qtrim) && (origSeq.length() != currSeq.getUnaligned().length())) { 
+                                       success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
+                               }
                                if(!success)                    {       trashCode += 'q';                                                               }
                        }
                        if(barcodes.size() != 0){