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

[mothur.git] / getseqscommand.h

diff --git a/getseqscommand.h b/getseqscommand.h
index 4fef8e795be355d23d1348f2ed323e225092b0f9..0f606ffb59ac884b46ac97d861aa3542786d1793 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -25,7 +25,8 @@ class GetSeqsCommand : public Command {
                string getCommandCategory()             { return "Sequence Processing";         }
                string getHelpString(); 
                string getCitation() { return "http://www.mothur.org/wiki/Get.seqs"; }
-       
+               string getDescription()         { return "gets sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
+
                int execute(); 
                void help() { m->mothurOut(getHelpString()); }  
        
@@ -35,6 +36,9 @@ class GetSeqsCommand : public Command {
                vector<string> outputNames;
                string accnosfile, accnosfile2, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
                bool abort, dups;
+    
+        //for debug
+        map<string, set<string> > sanity; //maps file type to names chosen for file. something like "fasta" -> vector<string>. If running in debug mode this is filled and we check to make sure all the files have the same names. If they don't we output the differences for the user.
                
                int readFasta();
                int readName();
@@ -45,6 +49,9 @@ class GetSeqsCommand : public Command {
                int readTax();
                int readQual();
                int compareAccnos();
+        int runSanityCheck();
+        int createMisMatchFile(ofstream&, string, string, set<string>, set<string>);
+
                
 };