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root/gclib/gclib/GAlnExtend.h
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# Line 5 | Line 5
5  
6   #include "GBase.h"
7   #include "GList.hh"
8 < #include <string.h>
8 > #include "gdna.h"
9  
10   //#define GDEBUG 1
11  
# Line 98 | Line 98
98  
99          if (GX_EDITOP_GET(oplast) == op) {
100              uint32 l=ops[opnum-1];
101 <            ops[opnum-1]=GX_EDITOP_CONS((GX_EDITOP_GET(l)),
101 >            ops[opnum-1]=GX_EDITOP_CONS((GX_EDITOP_GET(l)),
102                 (GX_EDITOP_VAL(l) + k));
103              }
104          else {
# Line 371 | Line 371
371             }
372  
373   #ifdef GDEBUG
374 <        void printAlignment(FILE* f, const char* sa, int sa_len,
374 >        void printAlignment(FILE* f, const char* sa, int sa_len,
375                       const char* sb, int sb_len) {
376                  //print seq A
377             char al[1024]; //display buffer for seq A
# Line 436 | Line 436
436         }
437   #endif
438    };
439 <  
439 >
440   struct GXAlnInfo {
441   const char *qseq;
442   int ql,qr;
# Line 613 | Line 613
613   };
614  
615  
616 < GXBandSet* collectSeeds_R(GList<GXSeed>& seeds, const char* seqa, int a_len, const char* seqb, int b_len); //for overlap at 3' end of seqb
616 > uint16 get6mer(char* p);
617 >
618 > GXBandSet* collectSeeds_R(GList<GXSeed>& seeds, const char* seqa, int a_len, GVec<uint16> amers[],
619 >         const char* seqb, int b_len); //for overlap at 3' end of seqb
620  
621 < GXBandSet* collectSeeds_L(GList<GXSeed>& seeds, const char* seqa, int a_len, const char* seqb, int b_len); //for overlap at 5' end of seqb
621 > GXBandSet* collectSeeds_L(GList<GXSeed>& seeds, const char* seqa, int a_len, GVec<uint16> amers[],
622 >        const char* seqb, int b_len); //for overlap at 5' end of seqb
623  
624   void printEditScript(GXEditScript* ed_script);
625  
# Line 713 | Line 717
717   GXAlnInfo* GreedyAlign(const char* q_seq,  int q_alnstart, const char* s_seq, int s_alnstart,
718          bool editscript=false, int reward=2, int penalty=3, int xdrop=8);
719  
720 < GXAlnInfo* match_LeftEnd(const char* seqa, int seqa_len, const char* seqb, int seqb_len,
721 <          CGreedyAlignData* gxmem=NULL, int min_pid=83);
722 < GXAlnInfo* match_RightEnd(const char* seqa, int seqa_len, const char* seqb, int seqb_len,
723 <          CGreedyAlignData* gxmem=NULL, int min_pid=73);
720 > GXAlnInfo* match_LeftEnd(const char* seqa, int seqa_len, GVec<uint16> amers[],
721 >           const char* seqb, int seqb_len, CGreedyAlignData* gxmem=NULL, int min_pid=83);
722 > GXAlnInfo* match_RightEnd(const char* seqa, int seqa_len, GVec<uint16> amers[],
723 >           const char* seqb, int seqb_len, CGreedyAlignData* gxmem=NULL, int min_pid=73);
724   #endif

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