added count file to chimera.uchime. found issue with uchime program that indicated...

[mothur.git] / pcrseqscommand.h

diff --git a/pcrseqscommand.h b/pcrseqscommand.h
index 07ca8d5e8ed486af362933896725cb48c28b3df2..baeca4eedc66ac9aa38acaa4b7d65bfebca56410 100644 (file)
--- a/pcrseqscommand.h
+++ b/pcrseqscommand.h
@@ -25,6 +25,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "pcr.seqs";    }
        string getCommandCategory()             { return "Sequence Processing";         }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Pcr.seqs"; }
        string getDescription()         { return "pcr.seqs"; }
@@ -43,9 +44,9 @@ private:
     
     vector<linePair> lines;
        bool getOligos(vector<vector<string> >&, vector<vector<string> >&, vector<vector<string> >&);
-    bool abort, keepprimer;
+    bool abort, keepprimer, keepdots;
        string fastafile, oligosfile, taxfile, groupfile, namefile, ecolifile, outputDir, nomatch;
-       int start, end, pdiffs, processors, length;
+       int start, end, processors, length;
        
     vector<string> revPrimer, outputNames;
        vector<string> primers;
@@ -79,11 +80,11 @@ struct pcrData {
        vector<string> primers;
     vector<string> revPrimer;
     set<string> badSeqNames;
-    bool keepprimer;
+    bool keepprimer, keepdots;
        
        
        pcrData(){}
-       pcrData(string f, string gf, string bfn, MothurOut* mout, string ol, string ec, vector<string> pr, vector<string> rpr, string nm, bool kp, int st, int en, int l, unsigned long long fst, unsigned long long fen) {
+       pcrData(string f, string gf, string bfn, MothurOut* mout, string ol, string ec, vector<string> pr, vector<string> rpr, string nm, bool kp, bool kd, int st, int en, int l, unsigned long long fst, unsigned long long fen) {
                filename = f;
         goodFasta = gf;
         badFasta = bfn;
@@ -94,6 +95,7 @@ struct pcrData {
         revPrimer = rpr;
         nomatch = nm;
         keepprimer = kp;
+        keepdots = kd;
                start = st;
                end = en;
         length = l;
@@ -216,8 +218,14 @@ static DWORD WINAPI MyPcrThreadFunction(LPVOID lpParam){
                         else{
                             //are you aligned
                             if (aligned) { 
-                                if (!pDataArray->keepprimer)    {  currSeq.padToPos(mapAligned[primerEnd]); } 
-                                else                {  currSeq.padToPos(mapAligned[primerStart]); }
+                                if (!pDataArray->keepprimer)    {  
+                                    if (pDataArray->keepdots)   { currSeq.filterToPos(mapAligned[primerEnd]);   }
+                                    else            { currSeq.setAligned(currSeq.getAligned().substr(mapAligned[primerEnd]));                                              }
+                                } 
+                                else                {  
+                                    if (pDataArray->keepdots)   { currSeq.filterToPos(mapAligned[primerStart]);  }
+                                    else            { currSeq.setAligned(currSeq.getAligned().substr(mapAligned[primerStart]));                                              }
+                                }
                             }else { 
                                 if (!pDataArray->keepprimer)    { currSeq.setAligned(currSeq.getUnaligned().substr(primerEnd)); } 
                                 else                { currSeq.setAligned(currSeq.getUnaligned().substr(primerStart)); } 
@@ -286,9 +294,14 @@ static DWORD WINAPI MyPcrThreadFunction(LPVOID lpParam){
                         else{ 
                             //are you aligned
                             if (aligned) { 
-                                if (!pDataArray->keepprimer)    {  currSeq.padFromPos(mapAligned[primerStart]); } 
-                                else                {  currSeq.padFromPos(mapAligned[primerEnd]); } 
-                            }
+                                if (!pDataArray->keepprimer)    {  
+                                    if (pDataArray->keepdots)   { currSeq.filterFromPos(mapAligned[primerStart]); }
+                                    else            { currSeq.setAligned(currSeq.getAligned().substr(0, mapAligned[primerStart]));   }
+                                } 
+                                else                {  
+                                    if (pDataArray->keepdots)   { currSeq.filterFromPos(mapAligned[primerEnd]); }
+                                    else            { currSeq.setAligned(currSeq.getAligned().substr(0, mapAligned[primerEnd]));   }
+                                }                             }
                             else { 
                                 if (!pDataArray->keepprimer)    { currSeq.setAligned(currSeq.getUnaligned().substr(0, primerStart));   } 
                                 else                { currSeq.setAligned(currSeq.getUnaligned().substr(0, primerEnd));     }
@@ -302,21 +315,38 @@ static DWORD WINAPI MyPcrThreadFunction(LPVOID lpParam){
                     else if (currSeq.getAligned().length() != pDataArray->length) {
                         pDataArray->m->mothurOut("[ERROR]: seqs are not the same length as ecoli seq. When using ecoli option your sequences must be aligned and the same length as the ecoli sequence.\n"); pDataArray->m->control_pressed = true; break; 
                     }else {
-                        currSeq.padToPos(pDataArray->start); 
-                        currSeq.padFromPos(pDataArray->end);
+                        if (pDataArray->keepdots)   { 
+                            currSeq.filterToPos(pDataArray->start); 
+                            currSeq.filterFromPos(pDataArray->end);
+                        }else {
+                            string seqString = currSeq.getAligned().substr(0, pDataArray->end);
+                            seqString = seqString.substr(pDataArray->start);
+                            currSeq.setAligned(seqString); 
+                        }
                     }
                 }else{ //using start and end to trim
                     //make sure the seqs are aligned
                     lengths.insert(currSeq.getAligned().length());
                     if (lengths.size() > 1) { pDataArray->m->mothurOut("[ERROR]: seqs are not aligned. When using start and end your sequences must be aligned.\n"); pDataArray->m->control_pressed = true; break; }
                     else {
-                        if (pDataArray->start != -1) { currSeq.padToPos(pDataArray->start); }
                         if (pDataArray->end != -1) {
                             if (pDataArray->end > currSeq.getAligned().length()) {  pDataArray->m->mothurOut("[ERROR]: end is longer than your sequence length, aborting.\n"); pDataArray->m->control_pressed = true; break; }
                             else {
-                                currSeq.padFromPos(pDataArray->end);
+                                if (pDataArray->keepdots)   { currSeq.filterFromPos(pDataArray->end); }
+                                else {
+                                    string seqString = currSeq.getAligned().substr(0, pDataArray->end);
+                                    currSeq.setAligned(seqString); 
+                                }
+                            }
+                        }
+                        if (pDataArray->start != -1) { 
+                            if (pDataArray->keepdots)   {  currSeq.filterToPos(pDataArray->start);  }
+                            else {
+                                string seqString = currSeq.getAligned().substr(pDataArray->start);
+                                currSeq.setAligned(seqString); 
                             }
                         }
+                        
                     }
                 }