pat's changes to seq.error command

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 2f8fbd7c499559bf65f9f5393982bd00dddfbcc3..21a5d41e759c761a3302340319c857544ffc313e 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -42,6 +42,9 @@ private:
        int stripBarcode(Sequence&, QualityScores&, int&);
        int stripForward(Sequence&, QualityScores&, int&);
        bool stripReverse(Sequence&, QualityScores&);
+       bool keepFirstTrim(Sequence&, QualityScores&);
+       bool removeLastTrim(Sequence&, QualityScores&);
+
        bool cullLength(Sequence&);
        bool cullHomoP(Sequence&);
        bool cullAmbigs(Sequence&);
@@ -54,7 +57,7 @@ private:
        
        bool flip, allFiles, qtrim;
        int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, comboStarts;
-       int qWindowSize, qWindowStep;
+       int qWindowSize, qWindowStep, keepFirst, removeLast;
        double qRollAverage, qThreshold, qWindowAverage, qAverage;
        vector<string> revPrimer, outputNames;
        set<string> filesToRemove;