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dbseq: Remove trailing spaces
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@pmenzel
pmenzel committed Oct 3, 2017
1 parent 935c9a3 commit 491a683
Showing 1 changed file with 31 additions and 31 deletions.
62 changes: 31 additions & 31 deletions dbseq.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ ref_loc_t RefSeq::LoadNextSeq(igzstream &fin) {
if(!param.gz_ref) return 0;
fin>>c; if(fin.eof()) return 0;
string::iterator z=_seq.begin();
_length=0;
_length=0;
fin>>_name; fin.getline(ch, 1000);
while(!fin.eof()) {
fin>>c; if(fin.eof()) break;
Expand Down Expand Up @@ -85,7 +85,7 @@ void RefSeq::BinSeq(OneBfa &a) {
void RefSeq::cBinSeq(OneBfa &a) {
a.n=(_length+(SEGLEN-1))/SEGLEN+BINSEQPAD; //SEGLENbp, bit(SEGLEN*2) for each element. put 2 extra elements at the 3'end to invoid overflow
/* int t=a.n*SEGLEN-_length;
cout << _length<< " "<<a.n << " t "<<t<<endl;
cout << _length<< " "<<a.n << " t "<<t<<endl;
if(t) {
string ts(t, 'N');
if(_seq.size()<_length+t) _seq.resize(_length+t);
Expand All @@ -107,7 +107,7 @@ void RefSeq::cBinSeq(OneBfa &a) {
}
//cout <<endl;
}


void RefSeq::UnmaskRegion() {
Block b, cb;
Expand All @@ -122,7 +122,7 @@ void RefSeq::UnmaskRegion() {
b.end=_seq.find_first_of(param.nx_nt, b.begin);
b.end = (b.end<=_length? b.end : _length);
if(b.end-b.begin <30) continue;
if((!_blocks.empty()) && (b.id==_blocks[_blocks.size()-1].id)
if((!_blocks.empty()) && (b.id==_blocks[_blocks.size()-1].id)
&& (b.begin - _blocks[_blocks.size()-1].end <5))
_blocks[_blocks.size()-1].end=b.end;
else {
Expand All @@ -134,15 +134,15 @@ void RefSeq::UnmaskRegion() {
//cout <<"bid "<<b.id<<" "<<b.begin<<" "<<b.end<<endl;
//cout <<"cbid "<<cb.id<<" "<<cb.begin<<" "<<cb.end<<endl;
}
}
}
}

void RefSeq::find_CCGG() {
bit32_t tmp_offset,tmp_max, seedloc, right=0xffffffffu, seglen; int i,j;
vector<ref_loc_t> tmpset_index_BSW[50], tmpset_index_BSC[50];
vector<pair<ref_loc_t, bit32_t> > tmp_CCGG_sites;
//vector<pair<ref_loc_t, bit32_t> >::iterator rit;

std::transform(_seq.begin(),_seq.end(),_seq.begin(),static_cast < int(*)(int) > (toupper));

tmp_offset=title[_count-1].rc_offset-param.seed_size;
Expand Down Expand Up @@ -170,12 +170,12 @@ void RefSeq::find_CCGG() {
for(j=0;j+1<tmp_CCGG_sites.size();++j) {
//for(rit=tmp_CCGG_sites.begin();rit!=tmp_CCGG_sites.end()-1&&tmp_CCGG_sites.size()>1;++rit) {
for(i=j+1,seglen=0;i<tmp_CCGG_sites.size();++i)
if((seglen=tmp_CCGG_sites[i].first+tmp_CCGG_sites[i].second-tmp_CCGG_sites[j].first)>=param.min_insert) break;
if((seglen=tmp_CCGG_sites[i].first+tmp_CCGG_sites[i].second-tmp_CCGG_sites[j].first)>=param.min_insert) break;
if(seglen>param.max_insert||seglen<param.min_insert) continue;
for(i=0,seedloc=tmp_CCGG_sites[j].first;i<param.max_seedseg_num&&seedloc<=tmp_max;i++,seedloc+=param.seed_size)
tmpset_index_BSW[i].push_back(seedloc);
}

for(j=1;j<tmp_CCGG_sites.size();++j) {
//for(rit=tmp_CCGG_sites.begin()+1;rit!=tmp_CCGG_sites.end()&&tmp_CCGG_sites.size()>1;++rit) {
for(i=j-1,seglen=0;i>=0;--i)
Expand All @@ -186,15 +186,15 @@ void RefSeq::find_CCGG() {
}

for(i=0;i<param.max_seedseg_num;i++) {
CCGG_index[i].push_back(tmpset_index_BSW[i]);
CCGG_index[i].push_back(tmpset_index_BSC[i]);
CCGG_index[i].push_back(tmpset_index_BSW[i]);
CCGG_index[i].push_back(tmpset_index_BSC[i]);
}
}

bool BlockComp(Block a, Block b) {return (a.id<b.id)||((a.id==b.id)&&(a.begin<b.begin));}

void RefSeq::Run_ConvertBinseq(ifstream &fin, igzstream &gzfin) {
param.max_seedseg_num=(FIXELEMENT-1)*SEGLEN/param.seed_size;
param.max_seedseg_num=(FIXELEMENT-1)*SEGLEN/param.seed_size;
_seq.resize(param.max_dbseq_size);
RefTitle r;
_count=0;
Expand All @@ -204,7 +204,7 @@ void RefSeq::Run_ConvertBinseq(ifstream &fin, igzstream &gzfin) {
r.size=_length;
r.rc_offset=((_length+(SEGLEN-1))/SEGLEN+BINSEQPAD)*SEGLEN;
title.push_back(r);

OneBfa a;
BinSeq(a);
bfa.push_back(a);
Expand All @@ -213,16 +213,16 @@ void RefSeq::Run_ConvertBinseq(ifstream &fin, igzstream &gzfin) {
total_num++;
sum_length+=_length;
// cout<<r.size<<endl;

//added by yxi, RC reference seq
title.push_back(r);
OneBfa ca;
cBinSeq(ca);
bfa.push_back(ca);
//UnmaskRegion();
_count++;
_count++;
//total_num++;
//sum_length+=_length;
//sum_length+=_length;
//cout<<"ref:"<<r.name<<endl;
if(param.RRBS_flag) find_CCGG();
}
Expand All @@ -249,7 +249,7 @@ void RefSeq::Run_ConvertBinseq(ifstream &fin, igzstream &gzfin) {
else {
cptr=copy(bfa[i].s, bfa[i].s+bfa[i].n, cptr);
delete [] bfa[i].s;
bfa[i].s=cptr-bfa[i].n;
bfa[i].s=cptr-bfa[i].n;
}
}

Expand All @@ -260,7 +260,7 @@ void RefSeq::Run_ConvertBinseq(ifstream &fin, igzstream &gzfin) {

_seq.clear(); //free ram
}

bit32_t RefSeq::s_MakeSeed_1(bit64_t *_m, int _a) {
return param.XT(((_m[0]<<(_a*2))|((_m[1]>>1)>>(63-_a*2)))>>param.seed_bits_lz);
//if(_a>=0) return param.XT((*_m>>_a)&param.seed_bits);
Expand Down Expand Up @@ -313,7 +313,7 @@ void RefSeq::CalKmerFreq() {
void RefSeq::t_CalKmerFreq(bit32_t ref_chain) {
bit64_t *_m; bit32_t i,j,i2, prefetch, ptr=0;
bit32_t dbs[PREFETCH_CAL_UNIT];
prefetch=PREFETCH_CAL_UNIT*param.index_interval;
prefetch=PREFETCH_CAL_UNIT*param.index_interval;
for(vector<Block>::iterator p=_blocks.begin(); p!=_blocks.end(); p++) {
if(p->id%2!=ref_chain) continue;
//cout<<"seg:"<<p->begin<<" "<<p->end<<endl;
Expand All @@ -324,19 +324,19 @@ void RefSeq::t_CalKmerFreq(bit32_t ref_chain) {
}
//cout<<"chain="<<ref_chain; for(jj=0;jj<PREFETCH_CAL_UNIT;jj++) cout<<" db["<<jj<<"]="<<dbs[jj]; cout<<endl;
for(i=(p->begin/param.index_interval)*param.index_interval; i<=i2; i+=param.index_interval,++ptr) {
index2[dbs[ptr%PREFETCH_CAL_UNIT]].n[ref_chain]++;
index2[dbs[ptr%PREFETCH_CAL_UNIT]].n[ref_chain]++;
j=s_MakeSeed_1(_m+(i+prefetch)/SEGLEN,(i+prefetch)%SEGLEN);
dbs[ptr%PREFETCH_CAL_UNIT]=j;
__builtin_prefetch(index2+j,1,0);
//cout<<"i="<<i<<" ptr="<<ptr<<" ptr_mod="<<(ptr%PREFETCH_CAL_UNIT)<<" current="<<dbs[ptr%PREFETCH_CAL_UNIT]<<" prefetch="<<j<<endl;
//for(jj=-PREFETCH_CAL_UNIT;jj<PREFETCH_CAL_UNIT*4;jj++) cout<<" "<<jj<<":"<<dbs[jj]; cout<<endl;
}
}
}
}

void RefSeq::AllocIndex() {
KmerLoc *v; KmerLoc2 *u;
bit32_t i, j, t, *ptr, block_size=1<<22, ptr_count=0;
bit32_t i, j, t, *ptr, block_size=1<<22, ptr_count=0;
if(param.RRBS_flag){
for(v=index,i=0; i<total_kmers; v++,i++) {
if(v->n1>0) {
Expand All @@ -351,7 +351,7 @@ void RefSeq::AllocIndex() {
mem_pool.push_back(ptr);
for(i=0,u=index2; i<total_kmers; i++,u++) {
t=u->n[1]+u->n[0]; kmer_count[i]=t;
if(t==0) continue;
if(t==0) continue;
if(ptr_count+t>=block_size-PREFETCH_LOOP) {
if(t>=block_size-PREFETCH_LOOP) {
u->loc1= new bit32_t[t+PREFETCH_LOOP];
Expand Down Expand Up @@ -404,7 +404,7 @@ void RefSeq::FillIndex() {
tmphit.chr=chr|(j<<16); _m=bfa[chr].s;
for(it=CCGG_index[j][chr].begin();it!=CCGG_index[j][chr].end();++it) {
z=index+s_MakeSeed_1(_m+(*it)/SEGLEN,(*it)%SEGLEN);
tmphit.loc=(*it);
tmphit.loc=(*it);
z->loc1[z->n1++]=tmphit;
}
if(param.pairend||param.chains) {
Expand All @@ -413,7 +413,7 @@ void RefSeq::FillIndex() {
for(it=CCGG_index[j][chr1].begin();it!=CCGG_index[j][chr1].end();++it) {
if(tmp_offset<*it) continue;
z=index+s_MakeSeed_1(_m+(int)(tmp_offset-*it)/SEGLEN,(tmp_offset-*it)%SEGLEN);
tmphit.loc=(tmp_offset-*it);
tmphit.loc=(tmp_offset-*it);
z->loc1[z->n1++]=tmphit;
}
}
Expand All @@ -439,11 +439,11 @@ void RefSeq::FillIndex() {
}

void RefSeq::t_FillIndex(bit32_t ref_chain) {
KmerLoc2 *z2; Hit tmphit;
KmerLoc2 *z2; Hit tmphit;
bit64_t *_m; bit32_t i2,j,i,prefetch, tmp=1-ref_chain, ptr=0;
bit32_t dbs[PREFETCH_CRT_UNIT];
prefetch=PREFETCH_CRT_UNIT*param.index_interval;
for(vector<Block>::iterator p=_blocks.begin(); p!=_blocks.end(); p++) {
for(vector<Block>::iterator p=_blocks.begin(); p!=_blocks.end(); p++) {
if(p->id%2!=ref_chain) continue;
tmphit.chr=p->id; _m=bfa[tmphit.chr].s;
i2=((p->end-param.seed_size)/param.index_interval)*param.index_interval;
Expand Down Expand Up @@ -471,7 +471,7 @@ void RefSeq::CreateIndex() {

void RefSeq::FinishIndex() {
bit32_t i;
if(param.RRBS_flag)
if(param.RRBS_flag)
for(i=0;i<param.max_seedseg_num;i++) CCGG_index[i].clear();
/*
for(i=0;i<total_kmers;i++) {
Expand Down Expand Up @@ -500,7 +500,7 @@ pair<ref_loc_t,bit32_t> RefSeq::CCGG_seglen(ref_id_t chr, ref_loc_t pos, int rea
//cout<<"pos:"<<pos<<"\tleft:"<<left<<" "<<CCGG_sites[chr2][left]<<"\tright:"<<right<<" "<<CCGG_sites[chr2][right]<<"\tmid:"<<mid<<" "<<CCGG_sites[chr2][mid]<<endl;
if((midval=(*CCGG_sites_chr)[mid].first)==pos) {//return pair<ref_loc_t,int>(pos+1,CCGG_sites[chr2][mid+1]-midval+2);
left=mid;right=mid+1;break;
}
}
else if(midval<pos) left=mid;
//if(CCGG_sites[chr2][mid]<=pos) left=mid;
else right=mid;
Expand All @@ -509,14 +509,14 @@ pair<ref_loc_t,bit32_t> RefSeq::CCGG_seglen(ref_id_t chr, ref_loc_t pos, int rea
//cout<<"pos:"<<pos<<"\tleft:"<<left<<" "<<CCGG_sites[chr2][left]<<"\tright:"<<right<<" "<<CCGG_sites[chr2][right]<<"\tmid:"<<mid<<" "<<CCGG_sites[chr2][mid]<<endl;
//for (mid=left-2;mid<left+3;mid++) cout<<"\t"<<CCGG_sites[chr2][mid]; cout<<endl;
seg_start=(*CCGG_sites_chr)[left].first;
while(((seg_end=(*CCGG_sites_chr)[right].first+(*CCGG_sites_chr)[right].second)<pos+readlen)&&(right<CCGG_sites_chr->size())) right++;
while(((seg_end=(*CCGG_sites_chr)[right].first+(*CCGG_sites_chr)[right].second)<pos+readlen)&&(right<CCGG_sites_chr->size())) right++;
//cout<<"pos:"<<pos<<"\tleft:"<<left<<" "<<CCGG_sites[chr2][left]<<"\tright:"<<right<<" "<<CCGG_sites[chr2][right]<<"\tmid:"<<mid<<" "<<CCGG_sites[chr2][mid]<<endl;}
//cout<<"ZP:"<<(seg_start+1)<<" ZL:"<<(seg_end-seg_start)<<endl;
//return pair<ref_loc_t,int>(CCGG_sites[chr2][left]+1, CCGG_sites[chr2][right]-CCGG_sites[chr2][left]+2);
return pair<ref_loc_t,bit32_t>(seg_start+1, seg_end-seg_start);
}
}



ref_loc_t RefSeq::hit2int(Hit h) {
return ref_anchor[h.chr/2]+h.loc;
}
Expand Down

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