X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimoligos.h;h=e3ea7d55537e323f3869a6157ff3aed4bbd99eea;hb=ece154e5d02f83d0ba6bf0438e3e1f085a2920bd;hp=8830dff57af8985c4f0e0bd4464f0860a46e8b81;hpb=ae57e166b2ed7b475ec3f466106bd76fabadd063;p=mothur.git diff --git a/trimoligos.h b/trimoligos.h index 8830dff..e3ea7d5 100644 --- a/trimoligos.h +++ b/trimoligos.h @@ -19,25 +19,34 @@ class TrimOligos { public: - TrimOligos(int,int, map, map, vector); //pdiffs, bdiffs, primers, barcodes, revPrimers + TrimOligos(int,int, map, map, vector); //pdiffs, bdiffs, primers, barcodes, revPrimers + TrimOligos(int,int, int, int, map, map, vector, vector, vector); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimers, linker, spacer ~TrimOligos(); int stripBarcode(Sequence&, int&); int stripBarcode(Sequence&, QualityScores&, int&); int stripForward(Sequence&, int&); - int stripForward(Sequence&, QualityScores&, int&); + int stripForward(Sequence&, QualityScores&, int&, bool); bool stripReverse(Sequence&); bool stripReverse(Sequence&, QualityScores&); + + bool stripLinker(Sequence&); + bool stripLinker(Sequence&, QualityScores&); + + bool stripSpacer(Sequence&); + bool stripSpacer(Sequence&, QualityScores&); private: - int pdiffs, bdiffs; + int pdiffs, bdiffs, ldiffs, sdiffs; map barcodes; map primers; vector revPrimer; + vector linker; + vector spacer; MothurOut* m;