--- gclib/GAlnExtend.h 2011/12/22 19:15:46 144 +++ gclib/GAlnExtend.h 2012/02/14 22:36:26 171 @@ -5,7 +5,7 @@ #include "GBase.h" #include "GList.hh" -#include +#include "gdna.h" //#define GDEBUG 1 @@ -98,7 +98,7 @@ if (GX_EDITOP_GET(oplast) == op) { uint32 l=ops[opnum-1]; - ops[opnum-1]=GX_EDITOP_CONS((GX_EDITOP_GET(l)), + ops[opnum-1]=GX_EDITOP_CONS((GX_EDITOP_GET(l)), (GX_EDITOP_VAL(l) + k)); } else { @@ -371,7 +371,7 @@ } #ifdef GDEBUG - void printAlignment(FILE* f, const char* sa, int sa_len, + void printAlignment(FILE* f, const char* sa, int sa_len, const char* sb, int sb_len) { //print seq A char al[1024]; //display buffer for seq A @@ -436,7 +436,7 @@ } #endif }; - + struct GXAlnInfo { const char *qseq; int ql,qr; @@ -613,9 +613,13 @@ }; -GXBandSet* collectSeeds_R(GList& seeds, const char* seqa, int a_len, const char* seqb, int b_len); //for overlap at 3' end of seqb +uint16 get6mer(char* p); + +GXBandSet* collectSeeds_R(GList& seeds, const char* seqa, int a_len, GVec amers[], + const char* seqb, int b_len); //for overlap at 3' end of seqb -GXBandSet* collectSeeds_L(GList& seeds, const char* seqa, int a_len, const char* seqb, int b_len); //for overlap at 5' end of seqb +GXBandSet* collectSeeds_L(GList& seeds, const char* seqa, int a_len, GVec amers[], + const char* seqb, int b_len); //for overlap at 5' end of seqb void printEditScript(GXEditScript* ed_script); @@ -713,8 +717,8 @@ GXAlnInfo* GreedyAlign(const char* q_seq, int q_alnstart, const char* s_seq, int s_alnstart, bool editscript=false, int reward=2, int penalty=3, int xdrop=8); -GXAlnInfo* match_LeftEnd(const char* seqa, int seqa_len, const char* seqb, int seqb_len, - CGreedyAlignData* gxmem=NULL, int min_pid=83); -GXAlnInfo* match_RightEnd(const char* seqa, int seqa_len, const char* seqb, int seqb_len, - CGreedyAlignData* gxmem=NULL, int min_pid=73); +GXAlnInfo* match_LeftEnd(const char* seqa, int seqa_len, GVec amers[], + const char* seqb, int seqb_len, CGreedyAlignData* gxmem=NULL, int min_pid=83); +GXAlnInfo* match_RightEnd(const char* seqa, int seqa_len, GVec amers[], + const char* seqb, int seqb_len, CGreedyAlignData* gxmem=NULL, int min_pid=73); #endif