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align.h: Remove trailing spaces
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@pmenzel
pmenzel committed Oct 2, 2017
1 parent 6311c0a commit 43aa7fa
Showing 1 changed file with 31 additions and 31 deletions.
62 changes: 31 additions & 31 deletions align.h
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Original file line number Diff line number Diff line change
@@ -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;

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