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root/gclib/gclib/GAlnExtend.h
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# Line 346 | Line 346
346         a_len=0;
347             b_len=0;
348             if (ed_script==NULL) return;
349 <           for (uint32 i=0; i<ed_script->opnum; i++) {
349 >           for (uint32 i=0; i<ed_script->opnum; i++) {
350                    int num=((ed_script->ops[i]) >> 2);
351                    char op_type = 3 - ( ed_script->ops[i] & gxEDIT_OP_MASK );
352                    if (op_type == 3 || op_type < 0 )
# Line 614 | Line 614
614  
615  
616   uint16 get6mer(char* p);
617 + void table6mers(const char* s, int slen, GVec<uint16>* amers[]);
618  
619 < GXBandSet* collectSeeds_R(GList<GXSeed>& seeds, const char* seqa, int a_len, GVec<uint16> amers[],
619 > GXBandSet* collectSeeds_R(GList<GXSeed>& seeds, const char* seqa, int a_len, GVec<uint16>* amers[],
620           const char* seqb, int b_len); //for overlap at 3' end of seqb
621  
622 < GXBandSet* collectSeeds_L(GList<GXSeed>& seeds, const char* seqa, int a_len, GVec<uint16> amers[],
622 > GXBandSet* collectSeeds_L(GList<GXSeed>& seeds, const char* seqa, int a_len, GVec<uint16>* amers[],
623          const char* seqb, int b_len); //for overlap at 5' end of seqb
624  
625   void printEditScript(GXEditScript* ed_script);
# Line 717 | Line 718
718   GXAlnInfo* GreedyAlign(const char* q_seq,  int q_alnstart, const char* s_seq, int s_alnstart,
719          bool editscript=false, int reward=2, int penalty=3, int xdrop=8);
720  
721 < GXAlnInfo* match_LeftEnd(const char* seqa, int seqa_len, GVec<uint16> amers[],
721 > GXAlnInfo* match_LeftEnd(const char* seqa, int seqa_len, GVec<uint16>* amers[],
722             const char* seqb, int seqb_len, CGreedyAlignData* gxmem=NULL, int min_pid=83);
723 < GXAlnInfo* match_RightEnd(const char* seqa, int seqa_len, GVec<uint16> amers[],
723 > GXAlnInfo* match_RightEnd(const char* seqa, int seqa_len, GVec<uint16>* amers[],
724             const char* seqb, int seqb_len, CGreedyAlignData* gxmem=NULL, int min_pid=73);
725   #endif

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