示例#1
0
bool ribo_profile::assign_reads(fp_list_t& fp_base_list, const unordered_set<int>& type_set)
{
  for (auto& r: fp_base_list) {
    // round 1: get candidate alignment loci
    if (r.used) continue;
    vector<position> loci;
    for (auto loc: r.al_loci) {
      rid_t refID(loc.refID); //transcript index
      rid_t t(get_transcript_index(refID));
      if (loc.start<0 or loc.stop>len(t)) {
        cout<<"profile index out of bound! readID:"<<*r.seqs.begin()<<" ";
        cout<<r.al_loci.size()<<" "<<refID<<" "<<loc.start<<"-"<<loc.stop<<" "<<len(t)<<endl;
        continue;
      }
      if (type_set.find(loc.type)!=type_set.end())
	loci.emplace_back(loc);
    } // for r.al_loci
    // no mappings of the desired type, move on to the next read
    if (loci.size() == 0) continue;
    // read processed mark as used
    r.used = true;
    // round 2: get transcript abundance
    vector<double> prob(loci.size(), 0);
    double tot_prob(0);
    for (size_t i=0; i!=prob.size(); ++i) {
      const position& loc(loci[i]);
      rid_t refID(loc.refID);
      rid_t t(get_transcript_index(refID));
      prob[i] = get_tot_abundance(t);
      tot_prob += prob[i];
    }
    // round 3: asign reads to loci proportional to loci prob
    for (size_t i=0; i!=prob.size(); ++i) {
      const position& loc(loci[i]);
      rid_t refID(loc.refID);
      rid_t t(get_transcript_index(refID));
      double count(r.count);
      if (prob.size()!=1)
	count *= prob[i] / tot_prob;
      for (rid_t base = loc.start; base != loc.stop; ++base) 
	add_read_count(t,base, count);
      add_tot_count(t, count);
    }
  }// for r: fp_base_list
  return check_tot_count(fp_base_list);
}
示例#2
0
文件: inspectio4.cpp 项目: yoyz/linux
size_t fread(void *ptr, size_t size, size_t nmemb,FILE *stream)
{
  int realsize=size*nmemb;
  int retsize;
  orig_fwrite_f_type orig_fread;
  //int gettimeofday(struct timeval *tv, struct timezone *tz);
  struct timeval tv0;
  struct timeval tv1;
  struct timezone tz;
  int fd;
  //mtx.lock();
  

  fd=fileno(stream);


  orig_fread  = (orig_fread_f_type)dlsym(RTLD_NEXT,"fread");

  gettimeofday(&tv0,&tz);
  retsize=orig_fread(ptr,size,nmemb,stream);
  gettimeofday(&tv1,&tz);

  std::string str;
  std::ostringstream oss;
  oss << "fread(" << ptr << "(" << fd << ")" << "," << size << "," << nmemb << "," << stream << ")="<< retsize << "\n"; 
  log.add(oss.str());


  if (size>=0)
    {
      if (myiio.existFd(fd)==-1)
	{
	  Ifile ifi;
	  ifi.setFd(fd);
	  //ifi.setName(std::string("UNKNOWN-FWRITE"));
	  ifi.setName(getStrFDInfo(fd));
	  ifi.setState(IOBYFILE_WRITE);
	  myiio.iiof.push_back(ifi);
	}
      add_read_count(fd,retsize);
      add_read_time(fd,tv0,tv1);
    }
  //mtx.unlock();
  return retsize;
}
示例#3
0
文件: inspectio4.cpp 项目: yoyz/linux
ssize_t read(int fd, void *buf, size_t count)
{
  int size;
  int size_t_count=count;
  orig_read_f_type orig_read;
  //int gettimeofday(struct timeval *tv, struct timezone *tz);
  struct timeval tv0;
  struct timeval tv1;
  struct timezone tz;

  //mtx.lock(); 
  orig_read  = (orig_read_f_type)dlsym(RTLD_NEXT,"read");

  gettimeofday(&tv0,&tz);
  size=orig_read(fd,buf,count);
  gettimeofday(&tv1,&tz);

  std::string str;
  std::ostringstream oss;
  oss << "read(" << fd << "," << buf << "," << count << ")\n"; 
  log.add(oss.str());


  if (size>=0)
    {
      if (myiio.existFd(fd)==-1)
	{
	  Ifile ifi;
	  ifi.setFd(fd);
	  ifi.setName(getStrFDInfo(fd));
	  //ifi.setName(std::string("UNKNOWN-WRITE"));
	  ifi.setState(IOBYFILE_READ);
	  myiio.iiof.push_back(ifi);
	}
      add_read_count(fd,size);
      add_read_time(fd,tv0,tv1);
    }
  //mtx.unlock();
  return size;   
}