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 4561d28614c62686c42e29a9747b84d853537fd0..0f606ffb59ac884b46ac97d861aa3542786d1793 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -36,6 +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();
@@ -46,6 +49,9 @@ class GetSeqsCommand : public Command {
                int readTax();
                int readQual();
                int compareAccnos();
+        int runSanityCheck();
+        int createMisMatchFile(ofstream&, string, string, set<string>, set<string>);
+
                
 };