diff --git a/align.h b/align.h
index 7a2da1a..31787fd 100644
--- a/align.h
+++ b/align.h
@@ -14,7 +14,7 @@
 
 using namespace std;
 
-const unsigned int FIXSIZE=SEGLEN*FIXELEMENT; 
+const unsigned int FIXSIZE=SEGLEN*FIXELEMENT;
 typedef gHit HitArray[MAXHITS+1];
 typedef HitArray HitMatrix[MAXSNPS+1];
 
@@ -35,7 +35,7 @@ class SingleAlign {
 	int TrimLowQual();
 	void ConvertBinaySeq();
     int CountSeeds(RefSeq &ref, int n, bit32_t start);
-	
+
 	inline void CountMismatch(bit64_t *q, bit32_t offset, bit64_t *s);
 	void ClearHits();
 	int RunAlign(RefSeq &ref);
@@ -44,7 +44,7 @@ class SingleAlign {
 	void StringAlign(RefSeq &ref, string &os);
 	void Reverse_Seq();
 	void s_OutHit(int chain, int n, bit8_t nspsn, gHit *hit, int insert_size, RefSeq &ref, string &os);
-    
+
     //by yxi
     void SnpAlign(RefSeq &ref, bit32_t mode);
     int TrimAdapter();
@@ -55,7 +55,7 @@ class SingleAlign {
     inline bit32_t MismatchPattern0(bit64_t *q, bit64_t *s, bit32_t seglen_offset);
     inline bit32_t MismatchPattern1(bit64_t *q, bit64_t *s, bit32_t gap_index, bit32_t seglen_offset);
     bit32_t GapAlign(RefSeq &ref, bit32_t mode, bit32_t seed_pos);
-    //int MatchGap(bit32_t mmi1[], bit32_t mmi2[], bit32_t shift);    
+    //int MatchGap(bit32_t mmi1[], bit32_t mmi2[], bit32_t shift);
     inline bit32_t AddHit(RefSeq &ref, bit32_t w, bit32_t mode);
     gHit int2hit(RefSeq &ref, gHit gh, int gap_size, bit32_t gap_pos);
 
@@ -82,12 +82,12 @@ class SingleAlign {
     bit64_t tmp_seq, tmp_reg;
     bit32_t end_element, end_offset;
 	SeedArray xseeds[2][MAXSNPS+1];
-	bit32_t xseed_array[2][FIXSIZE-SEGLEN], xseedreg_array[2][FIXSIZE-SEGLEN];	
+	bit32_t xseed_array[2][FIXSIZE-SEGLEN], xseedreg_array[2][FIXSIZE-SEGLEN];
 	bit32_t x_cur_n_hit[2][MAXSNPS+1], *_cur_n_hit, *_cur_n_chit;
 	bit32_t xseed_start_array[2][MAXSNPS+1];
 
-    set<ref_loc_t> *hitset, *ghitset; //, *chitset; 
-    pair<int,int> xseedindex[2][MAXSNPS+1];	
+    set<ref_loc_t> *hitset, *ghitset; //, *chitset;
+    pair<int,int> xseedindex[2][MAXSNPS+1];
 	bit32_t mm_index[2*MAXGAPS+1][MAXSNPS+1];
 	char cigar[16];
 	bit64_t total_candidates, total_reads, total_seeds;
@@ -103,7 +103,7 @@ class SingleAlign {
 	//local variables
 	string::iterator _sp;
 	string::reverse_iterator _sq;
-	
+
 	char _ch[1024];
     pair<ref_loc_t,bit32_t> seg_info;
     char _mapseq[256];
@@ -120,11 +120,11 @@ inline void SingleAlign::CountMismatch(bit64_t *q, bit32_t offset, bit64_t *s) {
     else {
     	if((tmp_snp=N_count+param.XM64((((*q)>>offset)&param.XC64(*s)^(*s))&((q[FIXELEMENT])>>offset)))>snp_thres) return;
     	for(bit32_t i=1;i<FIXELEMENT;i++) {
-    		if((tmp_snp+=param.XM64(((((q[i-1]<<1)<<(63-offset))|q[i]>>offset)&param.XC64(s[i])^s[i])&(((q[FIXELEMENT-1+i]<<1)<<(63-offset))|q[i+FIXELEMENT]>>offset)))>snp_thres) return; 
+    		if((tmp_snp+=param.XM64(((((q[i-1]<<1)<<(63-offset))|q[i]>>offset)&param.XC64(s[i])^s[i])&(((q[FIXELEMENT-1+i]<<1)<<(63-offset))|q[i+FIXELEMENT]>>offset)))>snp_thres) return;
     	}
     	/*
         tmp_snp=N_count;
-        for(bit32_t i=0;i<5;i++) { 
+        for(bit32_t i=0;i<5;i++) {
         	tmp=(s[i]<<offset)|((s[i+1]>>(63-offset))>>1);
             if((tmp_snp+=param.XM64((q[i]&param.XC64(tmp)^tmp)&q[i+5]))>snp_thres) return;
 		}
@@ -137,7 +137,7 @@ inline bit32_t SingleAlign::MismatchPattern0(bit64_t *q, bit64_t *s, bit32_t off
     bit32_t *mm_array; int i, j,jj, ss=0;
     //cout<<"in MMpattern()  gap_index:"<<gap_index<<endl;
     //cout<<" offset="<<seglen_offset<<" end_element="<<end_element<<" end_offset="<<end_offset<<endl;
-    mm_array=mm_index[0]; 
+    mm_array=mm_index[0];
     //cout<<"ss="<<ss<<" tmp_snp="<<tmp_snp<<" snp_thres="<<snp_thres<<endl;
     for(i=0;i<end_element;i++) {
 		tmp=(s[i]<<offset)|((s[i+1]>>(63-offset))>>1);
@@ -148,7 +148,7 @@ inline bit32_t SingleAlign::MismatchPattern0(bit64_t *q, bit64_t *s, bit32_t off
             jj=__builtin_clzll(tmp)>>1; j+=jj+1;
             //param.disp_bin64(tmp);
             //cout<<"\ti="<<i<<" j="<<j<<" jj="<<jj<< "ss="<<ss+1<<endl;
-            mm_array[ss++]=j; 
+            mm_array[ss++]=j;
             if(ss>(int)snp_thres-2) return j;
             tmp<<=2; tmp<<=(jj<<1);
         }
@@ -161,7 +161,7 @@ inline bit32_t SingleAlign::MismatchPattern0(bit64_t *q, bit64_t *s, bit32_t off
     j=(int)(i*SEGLEN)-1;
     while(tmp) {
         jj=__builtin_clzll(tmp)>>1; j+=jj+1;
-        mm_array[ss++]=j; 
+        mm_array[ss++]=j;
         if(ss>(int)snp_thres-2) return j;
         tmp<<=2; tmp<<=(jj<<1);
     }
@@ -172,62 +172,62 @@ inline bit32_t SingleAlign::MismatchPattern0(bit64_t *q, bit64_t *s, bit32_t off
 inline bit32_t SingleAlign::MismatchPattern1(bit64_t *q, bit64_t *s, bit32_t gap_index, bit32_t offset) {
     register bit64_t tmp; register bit32_t shift;
     bit32_t *mm_array; int i,ii, j,jj, ss=0;
-    //cout<<"in MMpattern()  gap_index:"<<gap_index<<endl;             
+    //cout<<"in MMpattern()  gap_index:"<<gap_index<<endl;
     //cout<<"shift="<<(1-((int)gap_index%2)*2)*((int)gap_index+1)/2<<" offset="<<seglen_offset<<" end_element="<<end_element;
-    //cout<<" end_offset="<<end_offset<<endl;  
+    //cout<<" end_offset="<<end_offset<<endl;
     //for(i=0;i<5;i++) disp_bfa64(param.swap_endian64(q[i])); cout<<endl;
     //for(i=0;i<5;i++) disp_bfa64(param.swap_endian64(s[i])); cout<<endl;
-    mm_array=mm_index[gap_index]; 
-    for(i=end_element,ii=0;i>=0;i--,ii+=SEGLEN) { 
+    mm_array=mm_index[gap_index];
+    for(i=end_element,ii=0;i>=0;i--,ii+=SEGLEN) {
 		tmp=(s[i]<<offset)|((s[i+1]>>(63-offset))>>1);
         if(param.nt3) tmp=q[i]^param.XT64(tmp);
         else tmp^=q[i]&param.XC64(tmp);
         shift=end_offset*(i==end_element); tmp=(tmp>>shift)<<shift;
-        j=ii-(int) (end_offset>>1)-1; 
+        j=ii-(int) (end_offset>>1)-1;
         while(tmp) {
             jj=__builtin_ctzll(tmp)>>1; j+=jj+1;
-            //cout<<"jj="<<jj<<" j="<<j<<" "; param.disp_bin64(tmp); 
+            //cout<<"jj="<<jj<<" j="<<j<<" "; param.disp_bin64(tmp);
             //cout<<" mm_array["<<ss<<"]="<<j<<endl;
-            mm_array[ss++]=j; 
+            mm_array[ss++]=j;
             if(ss>(int)snp_thres-2) return 1;
             tmp>>=2; tmp>>=(jj<<1);
         }
     }
     for(;ss<=(int)snp_thres-2;ss++) mm_array[ss]=map_readlen;
     return map_readlen;
-}   
+}
 
 /*
 inline bit32_t SingleAlign::MismatchPattern1(bit64_t *q, bit64_t *s, bit32_t gap_index, bit32_t seglen_offset) {
     register bit64_t tmp; register bit32_t shift;
     bit32_t *mm_array; int i,ii, j,jj, ss=0, end_element, right, end_offset, max0, offset=seglen_offset<<1;
-    end_element=(map_readlen+seglen_offset-1)/SEGLEN; 
+    end_element=(map_readlen+seglen_offset-1)/SEGLEN;
     right=(map_readlen+seglen_offset-1)%SEGLEN+1;  end_offset=SEGLEN-right;
-    //cout<<"in MMpattern()  gap_index:"<<gap_index<<endl;             
+    //cout<<"in MMpattern()  gap_index:"<<gap_index<<endl;
     //cout<<"shift="<<(1-((int)gap_index%2)*2)*((int)gap_index+1)/2<<" offset="<<seglen_offset<<" end_element="<<end_element;
-    //cout<<" end_offset="<<end_offset<<endl;  
+    //cout<<" end_offset="<<end_offset<<endl;
     //for(i=0;i<5;i++) disp_bfa64(param.swap_endian64(q[i])); cout<<endl;
     //for(i=0;i<5;i++) disp_bfa64(param.swap_endian64(s[i])); cout<<endl;
-    mm_array=mm_index[gap_index]; 
+    mm_array=mm_index[gap_index];
 	for(i=end_element,ii=0;i>=0;i--,ii+=SEGLEN) {
-        tmp_seq=(i>0)*(q[i-(i>0)]<<63-offset)<<1; 
+        tmp_seq=(i>0)*(q[i-(i>0)]<<63-offset)<<1;
         if(param.nt3) tmp=(tmp_seq|q[i]>>offset)^param.XT64(s[i]);
 		else tmp=(tmp_seq|q[i]>>offset)&param.XC64(s[i])^s[i];
 		shift=seglen_offset*2*(i==0); tmp=(tmp<<shift)>>shift;
 		shift=end_offset*2*(i==end_element); tmp=(tmp>>shift)<<shift;
-		j=ii-(int) end_offset-1; 
+		j=ii-(int) end_offset-1;
 		while(tmp) {
 			jj=__builtin_ctzll(tmp)>>1; j+=jj+1;
-			//cout<<"jj="<<jj<<" j="<<j<<" "; param.disp_bin64(tmp); 
+			//cout<<"jj="<<jj<<" j="<<j<<" "; param.disp_bin64(tmp);
 			//cout<<" mm_array["<<ss<<"]="<<j<<endl;
-			mm_array[ss++]=j; 
+			mm_array[ss++]=j;
             if(ss>(int)snp_thres-2) return 1;
             tmp>>=2; tmp>>=(jj<<1);
         }
 	}
     for(;ss<=(int)snp_thres-2;ss++) mm_array[ss]=map_readlen;
     return map_readlen;
-}	
+}
 */
 inline bit32_t SingleAlign::AddHit(RefSeq &ref, bit32_t w, bit32_t mode) {
 	if((int)_ghit.loc<0) return 0; //underflow the start of refseq
@@ -242,7 +242,7 @@ inline bit32_t SingleAlign::AddHit(RefSeq &ref, bit32_t w, bit32_t mode) {
     xhits[read_chain_index][w][x_cur_n_hit[read_chain_index][w]++]=_ghit;
     //if(w==mode&&!param.pairend&&param.report_repeat_hits==0) if(_cur_n_hit[w]+_cur_n_chit[w]>1) return 1;
     if(_cur_n_hit[w]+_cur_n_chit[w]>=param.max_num_hits) {
-        if(w==0) return 1; 
+        if(w==0) return 1;
         else snp_thres=w-1;
 	}
     return 0;