--- 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 <string.h>
+#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<GXSeed>& 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<GXSeed>& seeds, const char* seqa, int a_len, GVec<uint16> amers[],
+	 const char* seqb, int b_len); //for overlap at 3' end of seqb
 
-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
+GXBandSet* collectSeeds_L(GList<GXSeed>& seeds, const char* seqa, int a_len, GVec<uint16> 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<uint16> amers[],
+	   const char* seqb, int seqb_len, CGreedyAlignData* gxmem=NULL, int min_pid=83);
+GXAlnInfo* match_RightEnd(const char* seqa, int seqa_len, GVec<uint16> amers[],
+	   const char* seqb, int seqb_len, CGreedyAlignData* gxmem=NULL, int min_pid=73);
 #endif