C++ BamAlignment::EditTag方法代码示例

int main ( int argc, char *argv[] ) { 

  struct parameters *param = 0;
  param = interface(param, argc, argv);


  //bam input and generate index if not yet 
  //-------------------------------------------------------------------------------------------------------+
  // BAM input (file or filenames?)                                                                        |
  //-------------------------------------------------------------------------------------------------------+
  char *fof = param->mapping_f;
  FILE *IN=NULL;
  char linefof[5000];
  int filecount=0;
  vector <string> fnames;

  if (strchr(fof,' ')!=NULL) {
    char *ptr;
    ptr=strtok(fof," ");
    while (ptr!=NULL) {
      fnames.push_back(ptr);
      filecount++;
      ptr=strtok(NULL," ");
    }
  } else {
    IN=fopen(fof,"rt");
    if (IN!=NULL) {
      long linecount=0;
      while (fgets(linefof,5000-1,IN)!=NULL) {
        linecount++;
        if (linefof[0]!='#' && linefof[0]!='\n') {
          char *ptr=strchr(linefof,'\n');
          if (ptr!=NULL && ptr[0]=='\n') {
            ptr[0]='\0';
          }
          FILE *dummy=NULL;
          dummy=fopen(linefof,"rt");
          if (dummy!=NULL) {     // seems to be a file of filenames...
            fclose(dummy);
            fnames.push_back(linefof);
            filecount++;
          } else if (filecount==0 || linecount>=1000-1) {  // seems to be a single file
            fnames.push_back(fof);
            filecount++;
            break;
          }
        }
      }
      fclose(IN);
    }
  }  //file or file name decided and stored in vector "fnames"

  cerr << "the input mapping files are:" << endl;
  vector <string>::iterator fit = fnames.begin();
  for(; fit != fnames.end(); fit++) {
    cerr << *fit << endl;
  }

  //-------------------------------------------------------------------------------------------------------+
  // end of file or filenames                                                                              |
  //-------------------------------------------------------------------------------------------------------+

  // open the BAM file(s)
  BamMultiReader reader;
  reader.Open(fnames);

  // get header & reference information
  string header = reader.GetHeaderText();
  RefVector refs = reader.GetReferenceData();


  // attempt to open BamWriter
  BamWriter writer;
  string outputBam = param->writer;
  if ( outputBam != "" ) {
    if ( !writer.Open(param->writer, header, refs) ) {
      cerr << "Could not open output BAM file" << endl;
      exit(0);
    }
  }


  BamAlignment bam;
  while (reader.GetNextAlignment(bam)) { //change RG 

    string rg = "RG";
    string rgType = "Z";
    string rgValue = "1";
    bam.EditTag(rg,rgType,rgValue);

    writer.SaveAlignment(bam);
    
  }  // read a bam

  return 0;

} //main

//.........这里部分代码省略.........
	    logf << '\n';
	  }
	  modified_alignment_readcounter++;
	}
	else
	{
            if (logf.is_open ())
	    {
	      logf << alignment.Name << '\t' << alignment.IsReverseStrand() << '\t' << alignment.RefID << '\t' << setfill ('0') << setw (8) << orig_position << '\t' << "UNMOD";
              if (clipfail)
	        logf << " NOCLIP";
	      logf << '\n';
	    }
	}

        if (aligner.verbose_){
          cout << alignment.Name << endl;
          cout << "------------------------------------------" << endl;
          // Wait for input to continue or quit program
          if (input.size() == 0)
            input = 'x';
          else if (input[0] != 'c' and input[0] != 'C')
            getline(cin, input);
          if (input.size()>0){
            if (input[0] == 'q' or input[0] == 'Q')
              return 1;
            else if (input[0] == 's' or input[0] == 'S')
              aligner.verbose_ = false;
          }
        }

        // Finally update alignment information
        alignment.CigarData = new_cigar_data;
        alignment.EditTag("MD", "Z" , new_md_tag);

      } // end of CreateRef else if
      else {
	switch (aligner.GetCreateRefError ())
	{
	  case Realigner::CR_ERR_RECREATE_REF:
            if (logf.is_open ())
	      logf << alignment.Name << '\t' << alignment.IsReverseStrand() << '\t' << alignment.RefID << '\t' << setfill ('0') << setw (8) << orig_position << '\t' << "RECRERR" << '\n';
	    error_recreate_ref_readcount++;
	    break;
	  case Realigner::CR_ERR_CLIP_ANCHOR:
            if (logf.is_open ())
	      logf << alignment.Name << '\t' << alignment.IsReverseStrand() << '\t' << alignment.RefID << '\t' << setfill ('0') << setw (8) << orig_position << '\t' << "CLIPERR" << '\n';
	    error_clip_anchor_readcount++;
	    break;
	  default:
		  //  On a good run this writes way too many reads to the log file - don't want to create a too large txt file
          //  if (logf.is_open ())
	      //logf << alignment.Name << '\t' << alignment.IsReverseStrand() << '\t' << alignment.RefID << '\t' << setfill ('0') << setw (8) << orig_position << '\t' << "PERFECT" << '\n';
	    already_perfect_readcount++;
	    break;
	}
	
	if (aligner.verbose_) {
	  cout << alignment.Name << endl;
	  cout << "------------------------------------------" << endl;
	  // Wait for input to continue or quit program
	  if (input.size() == 0)
	    input = 'x';
	  else if (input[0] != 'c' and input[0] != 'C')
	    getline(cin, input);
	  if (input.size()>0){