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C++ BamMultiReader类代码示例

本文整理汇总了C++中BamMultiReader的典型用法代码示例。如果您正苦于以下问题:C++ BamMultiReader类的具体用法?C++ BamMultiReader怎么用?C++ BamMultiReader使用的例子?那么, 这里精选的类代码示例或许可以为您提供帮助。


在下文中一共展示了BamMultiReader类的11个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的C++代码示例。

示例1: if

bool ConvertTool::ConvertToolPrivate::Run(void) {
 
    // ------------------------------------
    // initialize conversion input/output
        
    // set to default input if none provided
    if ( !m_settings->HasInput ) 
        m_settings->InputFiles.push_back(Options::StandardIn());
    
    // open input files
    BamMultiReader reader;
    if ( !reader.Open(m_settings->InputFiles) ) {
        cerr << "bamtools convert ERROR: could not open input BAM file(s)... Aborting." << endl;
        return false;
    }

    // if input is not stdin & a region is provided, look for index files
    if ( m_settings->HasInput && m_settings->HasRegion ) {
        if ( !reader.LocateIndexes() ) {
            cerr << "bamtools convert ERROR: could not locate index file(s)... Aborting." << endl;
            return false;
        }
    }

    // retrieve reference data
    m_references = reader.GetReferenceData();

    // set region if specified
    BamRegion region;
    if ( m_settings->HasRegion ) {
        if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {

            if ( reader.HasIndexes() ) {
                if ( !reader.SetRegion(region) ) {
                    cerr << "bamtools convert ERROR: set region failed. Check that REGION describes a valid range" << endl;
                    reader.Close();
                    return false;
                }
            }

        } else {
            cerr << "bamtools convert ERROR: could not parse REGION: " << m_settings->Region << endl;
            cerr << "Check that REGION is in valid format (see documentation) and that the coordinates are valid"
                 << endl;
            reader.Close();
            return false;
        }
    }
        
    // if output file given
    ofstream outFile;
    if ( m_settings->HasOutput ) {
      
        // open output file stream
        outFile.open(m_settings->OutputFilename.c_str());
        if ( !outFile ) {
            cerr << "bamtools convert ERROR: could not open " << m_settings->OutputFilename
                 << " for output" << endl;
            return false; 
        }
        
        // set m_out to file's streambuf
        m_out.rdbuf(outFile.rdbuf()); 
    }
    
    // -------------------------------------
    // do conversion based on format
    
     bool convertedOk = true;
    
    // pileup is special case
    // conversion not done per alignment, like the other formats
    if ( m_settings->Format == FORMAT_PILEUP )
        convertedOk = RunPileupConversion(&reader);
    
    // all other formats
    else {
    
        bool formatError = false;
        
        // set function pointer to proper conversion method
        void (BamTools::ConvertTool::ConvertToolPrivate::*pFunction)(const BamAlignment&) = 0;
        if      ( m_settings->Format == FORMAT_BED )   pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintBed;
        else if ( m_settings->Format == FORMAT_FASTA ) pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintFasta;
        else if ( m_settings->Format == FORMAT_FASTQ ) pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintFastq;
        else if ( m_settings->Format == FORMAT_JSON )  pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintJson;
        else if ( m_settings->Format == FORMAT_SAM )   pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintSam;
        else if ( m_settings->Format == FORMAT_YAML )  pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintYaml;
        else { 
            cerr << "bamtools convert ERROR: unrecognized format: " << m_settings->Format << endl;
            cerr << "Please see documentation for list of supported formats " << endl;
            formatError = true;
            convertedOk = false;
        }
        
        // if format selected ok
        if ( !formatError ) {
        
            // if SAM format & not omitting header, print SAM header first
            if ( (m_settings->Format == FORMAT_SAM) && !m_settings->IsOmittingSamHeader ) 
//.........这里部分代码省略.........
开发者ID:alecchap,项目名称:bamtools,代码行数:101,代码来源:bamtools_convert.cpp

示例2: Run

int CountTool::Run(int argc, char* argv[]) { 

    // parse command line arguments
    Options::Parse(argc, argv, 1);

    // if no '-in' args supplied, default to stdin
    if ( !m_settings->HasInput ) 
        m_settings->InputFiles.push_back(Options::StandardIn());
    
    // open reader without index
    BamMultiReader reader;
    if (!reader.Open(m_settings->InputFiles, false, true)) {
        cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl;
        return 1;
    }

    // alignment counter
    BamAlignment al;
    int alignmentCount(0);
    
    // if no region specified, count entire file 
    if ( !m_settings->HasRegion ) {
        while ( reader.GetNextAlignmentCore(al) ) 
            ++alignmentCount;
    }
    
    // otherwise attempt to use region as constraint
    else {
        
        // if region string parses OK
        BamRegion region;
        if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {

            // attempt to re-open reader with index files
            reader.Close();
            bool openedOK = reader.Open(m_settings->InputFiles, true, true );
            
            // if error
            if ( !openedOK ) {
                cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl;
                return 1;
            }
            
            // if index data available, we can use SetRegion
            if ( reader.IsIndexLoaded() ) {
              
                // attempt to use SetRegion(), if failed report error
                if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
                    cerr << "ERROR: Region requested, but could not set BamReader region to REGION: " << m_settings->Region << " Aborting." << endl;
                    reader.Close();
                    return 1;
                } 
              
                // everything checks out, just iterate through specified region, counting alignments
                while ( reader.GetNextAlignmentCore(al) )
                    ++alignmentCount;
            } 
            
            // no index data available, we have to iterate through until we
            // find overlapping alignments
            else {
                while( reader.GetNextAlignmentCore(al) ) {
                    if ( (al.RefID >= region.LeftRefID)  && ( (al.Position + al.Length) >= region.LeftPosition ) &&
                          (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) ) 
                    {
                        ++alignmentCount;
                    }
                }
            }
        } 
        
        // error parsing REGION string
        else {
            cerr << "ERROR: Could not parse REGION - " << m_settings->Region << endl;
            cerr << "Be sure REGION is in valid format (see README) and that coordinates are valid for selected references" << endl;
            reader.Close();
            return 1;
        }
    }
    
    // print results 
    cout << alignmentCount << endl;
    
    // clean & exit
    reader.Close();
    return 0;
}
开发者ID:joshuashen,项目名称:bamtools,代码行数:87,代码来源:bamtools_count.cpp

示例3: if

bool ConvertTool::ConvertToolPrivate::Run(void) {
 
    // ------------------------------------
    // initialize conversion input/output
        
    // set to default input if none provided
    if ( !m_settings->HasInput ) 
        m_settings->InputFiles.push_back(Options::StandardIn());
    
    // open input files
    BamMultiReader reader;
    if ( !m_settings->HasInput ) { // don't attempt to open index for stdin
        if ( !reader.Open(m_settings->InputFiles, false) ) {
            cerr << "Could not open input files" << endl;
            return false;
        }
    } else {
        if ( !reader.Open(m_settings->InputFiles, true) ) {
            if ( !reader.Open(m_settings->InputFiles, false) ) {
                cerr << "Could not open input files" << endl;
                return false;
            } else {
                cerr << "Opened reader without index file, jumping is disabled." << endl;
            }
        }
    }
    m_references = reader.GetReferenceData();

    // set region if specified
    BamRegion region;
    if ( m_settings->HasRegion ) {
        if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
            if ( !reader.SetRegion(region) ) {
                cerr << "Could not set BamReader region to REGION: " << m_settings->Region << endl;
                return false;
            }
        } else {
            cerr << "Could not parse REGION: " << m_settings->Region << endl;
            return false;
        }
    }
        
    // if output file given
    ofstream outFile;
    if ( m_settings->HasOutput ) {
      
        // open output file stream
        outFile.open(m_settings->OutputFilename.c_str());
        if ( !outFile ) {
            cerr << "Could not open " << m_settings->OutputFilename << " for output" << endl; 
            return false; 
        }
        
        // set m_out to file's streambuf
        m_out.rdbuf(outFile.rdbuf()); 
    }
    
    // -------------------------------------
    // do conversion based on format
    
     bool convertedOk = true;
    
    // pileup is special case
    // conversion not done per alignment, like the other formats
    if ( m_settings->Format == FORMAT_PILEUP )
        convertedOk = RunPileupConversion(&reader);
    
    // all other formats
    else {
    
        bool formatError = false;
        
        // set function pointer to proper conversion method
        void (BamTools::ConvertTool::ConvertToolPrivate::*pFunction)(const BamAlignment&) = 0;
        if      ( m_settings->Format == FORMAT_BED )      pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintBed;
        else if ( m_settings->Format == FORMAT_BEDGRAPH ) pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintBedGraph;
        else if ( m_settings->Format == FORMAT_FASTA )    pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintFasta;
        else if ( m_settings->Format == FORMAT_FASTQ )    pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintFastq;
        else if ( m_settings->Format == FORMAT_JSON )     pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintJson;
        else if ( m_settings->Format == FORMAT_SAM )      pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintSam;
        else if ( m_settings->Format == FORMAT_WIGGLE )   pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintWiggle;
        else if ( m_settings->Format == FORMAT_YAML )     pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintYaml;
        else { 
            cerr << "Unrecognized format: " << m_settings->Format << endl;
            cerr << "Please see help|README (?) for details on supported formats " << endl;
            formatError = true;
            convertedOk = false;
        }
        
        // if format selected ok
        if ( !formatError ) {
        
            // if SAM format & not omitting header, print SAM header first
            if ( (m_settings->Format == FORMAT_SAM) && !m_settings->IsOmittingSamHeader ) 
                m_out << reader.GetHeaderText();
            
            // iterate through file, doing conversion
            BamAlignment a;
            while ( reader.GetNextAlignment(a) )
              (this->*pFunction)(a);
//.........这里部分代码省略.........
开发者ID:arq5x,项目名称:bamtools,代码行数:101,代码来源:bamtools_convert.cpp

示例4: main

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
开发者ID:ruping,项目名称:trick,代码行数:97,代码来源:changeBamRG.cpp

示例5: filelist

bool FilterTool::FilterToolPrivate::Run(void) {
    
    // set to default input if none provided
    if ( !m_settings->HasInput && !m_settings->HasInputFilelist )
        m_settings->InputFiles.push_back(Options::StandardIn());

    // add files in the filelist to the input file list
    if ( m_settings->HasInputFilelist ) {

        ifstream filelist(m_settings->InputFilelist.c_str(), ios::in);
        if ( !filelist.is_open() ) {
            cerr << "bamtools filter ERROR: could not open input BAM file list... Aborting." << endl;
            return false;
        }

        string line;
        while ( getline(filelist, line) )
            m_settings->InputFiles.push_back(line);
    }

    // initialize defined properties & user-specified filters
    // quit if failed
    if ( !SetupFilters() )
        return false;

    // open reader without index
    BamMultiReader reader;
    if ( !reader.Open(m_settings->InputFiles) ) {
        cerr << "bamtools filter ERROR: could not open input files for reading." << endl;
        return false;
    }

    // retrieve reader header & reference data
    const string headerText = reader.GetHeaderText();
    filterToolReferences = reader.GetReferenceData();
    
    // determine compression mode for BamWriter
    bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() &&
                              !m_settings->IsForceCompression );
    BamWriter::CompressionMode compressionMode = BamWriter::Compressed;
    if ( writeUncompressed ) compressionMode = BamWriter::Uncompressed;

    // open BamWriter
    BamWriter writer;
    writer.SetCompressionMode(compressionMode);
    if ( !writer.Open(m_settings->OutputFilename, headerText, filterToolReferences) ) {
        cerr << "bamtools filter ERROR: could not open " << m_settings->OutputFilename << " for writing." << endl;
        reader.Close();
        return false;
    }

    // if no region specified, filter entire file 
    BamAlignment al;
    if ( !m_settings->HasRegion ) {
        while ( reader.GetNextAlignment(al) ) {
            if ( CheckAlignment(al) ) 
                writer.SaveAlignment(al);
        }
    }
    
    // otherwise attempt to use region as constraint
    else {
        
        // if region string parses OK
        BamRegion region;
        if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {

            // attempt to find index files
            reader.LocateIndexes();

            // if index data available for all BAM files, we can use SetRegion
            if ( reader.HasIndexes() ) {

                // attempt to use SetRegion(), if failed report error
                if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
                    cerr << "bamtools filter ERROR: set region failed. Check that REGION describes a valid range" << endl;
                    reader.Close();
                    return false;
                } 
              
                // everything checks out, just iterate through specified region, filtering alignments
                while ( reader.GetNextAlignment(al) )
                    if ( CheckAlignment(al) ) 
                        writer.SaveAlignment(al);
                }
            
            // no index data available, we have to iterate through until we
            // find overlapping alignments
            else {
                while ( reader.GetNextAlignment(al) ) {
                    if ( (al.RefID >= region.LeftRefID)  && ((al.Position + al.Length) >= region.LeftPosition) &&
                         (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) ) 
                    {
                        if ( CheckAlignment(al) ) 
                            writer.SaveAlignment(al);
                    }
                }
            }
        } 
        
//.........这里部分代码省略.........
开发者ID:BIGLabHYU,项目名称:lumpy-sv,代码行数:101,代码来源:bamtools_filter.cpp

示例6: CropBam

int CropBamTool::CropBam()
{
    // open bam files
    BamMultiReader bamReader;
    bamReader.Open(bamFiles);

    // the dictionary of chromosomes
    RefVector genome = bamReader.GetReferenceData();

    // get the scanning window
    vector<tuple<int,int,int>> windows;
    int numWindows = GenericRegionTools::toScanWindow(genome, regionStrings, windows);

    unordered_set<string> readpool;

    // temporary struct for sequence object
    typedef struct {
        string name;
        int head_soft_clip;
        int tail_soft_clip;
        string seq;
        string qual;
    }cropbam_seq_t;

    // temporary struct for unique seqs
    map<string,list<cropbam_seq_t>> uniqueSeqPool;

    // lambda expression for output
    auto Output = [this](cropbam_seq_t &a){
          if (this->outFormat=="fasta"){
              cout << ">" << a.name << "\t"
                   << "head_soft_clip=" << a.head_soft_clip << "\t"
                   << "tail_soft_clip=" << a.tail_soft_clip << "\t"
                   << endl
                   << a.seq << endl;
          }
          if (this->outFormat=="fastq"){
              cout << "@" << a.name << "\t"
                   << "head_soft_clip=" << a.head_soft_clip << "\t"
                   << "tail_soft_clip=" << a.tail_soft_clip << "\t"
                   << endl
                   << a.seq << endl;
              cout << "+" << endl
                   << a.qual << endl;
          }
    };

    // loop over windows
    omp_set_dynamic(0);
    omp_set_num_threads(numThreads);
    #pragma omp parallel for shared(genome)
    for (int i=0; i<numWindows; i++)
    {
        clock_t tStart = clock();

        bamReader.Open(bamFiles);

        int wId = get<0>(windows[i]);
        int wLp = get<1>(windows[i]);
        int wRp = get<2>(windows[i]);

        if (verbose>=1) Verbose("process the window " + genome[wId].RefName + ":" + to_string(wLp+1) + "-" + to_string(wRp));

        // rewind the bam reader
        bamReader.Rewind();
        // set the region
        bamReader.SetRegion(wId, wLp, wId, wRp);

        int numReads = 0;
        // retrieve the alignment
        BamAlignment aln;
        while (bamReader.GetNextAlignment(aln))
        {
            // skip the alignment if it doesn't overlap the window
            if (aln.Position>=wRp || aln.GetEndPosition()<=wLp)
                continue;

            // skip the invalid alignment
            if (!isValidAlignment(aln, readLenThres, mapQualThres, alnFlagMarker))
                continue;

            // skip the alignment harboring too many mismatches
            if (!GenericBamAlignmentTools::validReadIdentity(aln, 1-alnIdenThres))
                continue;

            stringstream keyss;
            keyss << GenericBamAlignmentTools::getBamAlignmentName(aln) << "-"
                  << wId << "-" << wLp << "-" << wRp;
            string key = keyss.str();
            auto ptr = readpool.find(key);
            if (ptr!=readpool.end())
                continue;
            readpool.emplace(key);

            // get the partial read
            string readSegment, readQualSegment, genomeSegment;
            GenericBamAlignmentTools::getLocalAlignment(aln, wLp, wRp-wLp, readSegment, readQualSegment, genomeSegment);

            // add soft clip
            int hsc=0;
//.........这里部分代码省略.........
开发者ID:homopolymer,项目名称:PyroTools,代码行数:101,代码来源:CropBamTool.cpp

示例7: bbctools_create

int bbctools_create( BbcUtils::OptParser &optParser ) {
    const vector<string> cmdArgs = optParser.getArgs();

	// remove .bbc extension from bbc file root, if present
	string bbcfileRoot = optParser.getOptValue( "bbc" );
	int i = bbcfileRoot.size() - 4;
	if( i > 0 && bbcfileRoot.substr(i,4) == ".bbc" ) {
		bbcfileRoot = bbcfileRoot.substr(0,i);
	}
	bool f_bci = optParser.getOptBoolean("index");
	bool f_cbc = optParser.getOptBoolean("coarse");

	string targetRegions   = optParser.getOptValue("regions");
	string annotationFields = optParser.getOptValue( "annotationFields");
	vector<string> auxRegionSplit = BbcUtils::mapToPairList(annotationFields);

	string  sumstatsFile = optParser.getOptValue("sumStats");
	string  covstatsFile = optParser.getOptValue("covStats");
	string  readOrigFile = optParser.getOptValue("readOrigin");
	string  readType     = optParser.getOptValue("readType");
	string  covDepths    = optParser.getOptValue("covDepths","-");
	double  minPcCov     = optParser.getOptNumber("minPcCov");
	int32_t primerLength = optParser.getOptInteger( "primerLength", (readType == "AmpliSeq" ? 30 : 0) );
	int32_t maxE2eEndGap = optParser.getOptInteger( "e2eGap", (readType == "AmpliSeq" ? 2 : 0) );

	bool   autoCreateBamIndex = optParser.getOptBoolean("autoCreateBamIndex");
	bool     samdepth         = optParser.getOptBoolean("samdepth");
	int32_t  filterQuality    = optParser.getOptInteger("minMAPQ");
	int32_t  minAlignLength   = optParser.getOptInteger("minAlignLength");
	bool     filterDuplicates = optParser.getOptBoolean("noDups");
	bool     filterUnique     = optParser.getOptBoolean("unique");
	uint32_t skipFlag         = filterDuplicates ? 0x704 : 0x304;
	uint16_t minMapQuality    = filterUnique ? 1 : filterQuality;

	bool onlyOnTargetReads = optParser.getOptBoolean("onTargetReads");
	bool onlyOnTargetBases = optParser.getOptBoolean("onTargetBases");

	// possible future options
	bool invertOnTarget = false;

	// check basic valid argument values and combinations
	int numOuts  = !bbcfileRoot.empty() + !covstatsFile.empty() + !sumstatsFile.empty() + !readOrigFile.empty();
	int numPipes = (bbcfileRoot == "-") + (covstatsFile == "-") + (sumstatsFile == "-") + (readOrigFile == "-");
	if( numOuts == 0 && !f_bci && !f_cbc ) {
		bbcfileRoot = "-";	// default if no other output specified
	} else if( numPipes > 1 ) {
		cerr << "Error: bbctools create: Only one file output (--covStats, --sumStats, --readOrigin or --bbc) may be piped to STDOUT." << endl;
		return -1;
	} else if( samdepth && numOuts ) {
		cerr << "Error: bbctools create: --samdepth (-s) option may only be used without other output options." << endl;
		return -1;
	}
	// check if single argument is a BBC file and leave open for reading if so
	BbcView bbcView;
	bool haveBbcFile = cmdArgs.size() == 1 && bbcView.Open( cmdArgs[0], true );
	bbcView.SelectPrintStream( samdepth ? "SAMDEPTH" : "BBCVIEW" );

	// check distinction between default and explicit no target regions - only for BBC input
	bool explicitNoTargetRegions = false;
	if( targetRegions == "-" ) {
		explicitNoTargetRegions = haveBbcFile;
		targetRegions = "";
	}
	if( targetRegions.empty() ) {
		if( onlyOnTargetBases && explicitNoTargetRegions && !invertOnTarget ) {
			cerr << "Warning: bbctools create --onTargetBases (-b) option with --regions '-' produces no coverage." << endl;
		} else if( onlyOnTargetReads ) {
			cerr << "Error: bbctools create --onTargetReads (-r) option requires a --regions file." << endl;
			return -1;
		}
	}
	// check for legal BBC create options
	if( f_bci || f_cbc ) {
		if( (bbcfileRoot.empty() || bbcfileRoot == "-") && !haveBbcFile ) {
			string opt = f_bci ? "--index (-i)" : "--coarse (-c)";
			cerr << "Error: bbctools create "+opt+" option requires the --bbc (-B) option or a BBC source file." << endl;
			return -1;
		}
	}
	BamMultiReader bamReader;
	if( haveBbcFile ) {
		// warn for options that do not work with BBC input
		if( filterQuality > 0 || filterDuplicates || filterUnique || minAlignLength ) {
			cerr << "Warning: SAM flag, alignment length and MAPQ filters ignored for BBC source file." << endl;
		}
		if( samdepth ) {
			cerr << "Error: --samdepth option is not supported for BBC source files." << endl;
			return -1;
		}
		if( !readOrigFile.empty() ) {
			cerr << "Error: --readOrigin option is not supported for BBC source files." << endl;
			return -1;
		}
	} else {
		// check / open for multiple BAM file inputs
		if ( !bamReader.Open(cmdArgs) ) {
			if( cmdArgs.size() == 1 ) cerr << "ERROR: Could not read input BAM file:";
			else cerr << "ERROR: Could not read all input BAM files:";
			// get and clean up bamtools error msg
			string errMsg = bamReader.GetErrorString();
//.........这里部分代码省略.........
开发者ID:biocyberman,项目名称:TS,代码行数:101,代码来源:BbcMain.cpp

示例8: file

bool MergeTool::MergeToolPrivate::Run(void) {

    // set to default input if none provided
    if ( !m_settings->HasInputBamFilename )
        m_settings->InputFiles.push_back(Options::StandardIn());

    // opens the BAM files (by default without checking for indexes)
    BamMultiReader reader;
    if ( !reader.Open(m_settings->InputFiles) ) {
        cerr << "bamtools merge ERROR: could not open input BAM file(s)... Aborting." << endl;
        return false;
    }

    // retrieve header & reference dictionary info
    std::string mergedHeader = reader.GetHeaderText();
    RefVector references = reader.GetReferenceData();

    // determine compression mode for BamWriter
    bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() &&
                               !m_settings->IsForceCompression );
    BamWriter::CompressionMode compressionMode = BamWriter::Compressed;
    if ( writeUncompressed ) compressionMode = BamWriter::Uncompressed;

    // open BamWriter
    BamWriter writer;
    writer.SetCompressionMode(compressionMode);
    if ( !writer.Open(m_settings->OutputFilename, mergedHeader, references) ) {
        cerr << "bamtools merge ERROR: could not open "
             << m_settings->OutputFilename << " for writing." << endl;
        reader.Close();
        return false;
    }

    // if no region specified, store entire contents of file(s)
    if ( !m_settings->HasRegion ) {
        BamAlignment al;
        while ( reader.GetNextAlignmentCore(al) )
            writer.SaveAlignment(al);
    }

    // otherwise attempt to use region as constraint
    else {

        // if region string parses OK
        BamRegion region;
        if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {

            // attempt to find index files
            reader.LocateIndexes();

            // if index data available for all BAM files, we can use SetRegion
            if ( reader.HasIndexes() ) {

                // attempt to use SetRegion(), if failed report error
                if ( !reader.SetRegion(region.LeftRefID,
                                       region.LeftPosition,
                                       region.RightRefID,
                                       region.RightPosition) )
                {
                    cerr << "bamtools merge ERROR: set region failed. Check that REGION describes a valid range"
                         << endl;
                    reader.Close();
                    return false;
                }

                // everything checks out, just iterate through specified region, storing alignments
                BamAlignment al;
                while ( reader.GetNextAlignmentCore(al) )
                    writer.SaveAlignment(al);
            }

            // no index data available, we have to iterate through until we
            // find overlapping alignments
            else {
                BamAlignment al;
                while ( reader.GetNextAlignmentCore(al) ) {
                    if ( (al.RefID >= region.LeftRefID)  && ( (al.Position + al.Length) >= region.LeftPosition ) &&
                         (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
                    {
                        writer.SaveAlignment(al);
                    }
                }
            }
        }

        // error parsing REGION string
        else {
            cerr << "bamtools merge ERROR: could not parse REGION - " << m_settings->Region << endl;
            cerr << "Check that REGION is in valid format (see documentation) and that the coordinates are valid"
                 << endl;
            reader.Close();
            writer.Close();
            return false;
        }
    }

    // clean & exit
    reader.Close();
    writer.Close();
    return true;
//.........这里部分代码省略.........
开发者ID:alecchap,项目名称:bamtools,代码行数:101,代码来源:bamtools_merge.cpp

示例9: main

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

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

  //region file input (the region file should be sorted as the same way as the bam file)
  ifstream region_f;
  region_f.open(param->region_f, ios_base::in);  // the region file is opened

  //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();

  if ( ! reader.LocateIndexes() )     // opens any existing index files that match our BAM files
    reader.CreateIndexes();         // creates index files for BAM files that still lack one


  // locus bias
  struct lb empty_profile = {0,0,0,0};
  vector <struct lb> locus_b(1000, empty_profile);
  // output locus bias file
  string locus_bias_set = param->lbias;
  ofstream locus_bias;
  if ( locus_bias_set != "" ) {
    locus_bias.open(param->lbias);
    if ( !locus_bias ) {
      cerr << "can not open locus_bias file.\n";
      exit(0);
    }
  }

  //should decide which chromosome
  string line;
  string old_chr = "SRP";
  string type = param->type;

  //whether do some position-level pile-up stuff
  bool posc = false;
  ofstream posc_f;
  ofstream chrmap_f;
//.........这里部分代码省略.........
开发者ID:Cemily,项目名称:TRUP,代码行数:101,代码来源:Rseq_bam_reads2expr.cpp

示例10: ogeNameThread

int FileReader::runInternal()
{
    ogeNameThread("am_FileReader");

    if(!format_specified)
        format = deduceFileFormat();

    if(format == FORMAT_BAM)
    {
        BamMultiReader reader;
        
        if(!reader.Open(filenames)) {
            cerr << "Error opening BAM files." << endl;
            reader.Close();
            return -1;
        }
        
        header = reader.GetHeader();
        references = reader.GetReferenceData();
        open = true;
        
        BamAlignment * al;
        
        while(true)
        {
            if(load_string_data)
                al = reader.GetNextAlignment();
            else
                al = reader.GetNextAlignmentCore();

            if(!al)
                break;
            
            putOutputAlignment(al);
        }
        
        reader.Close();
    } else if(format == FORMAT_SAM) {
        
        vector<SamReader> readers;
        
        SamHeader first_header;

        // before doing any reading, open the files to
        // verify they are the right format, etc.
        for(int i = 0; i < filenames.size(); i++) {
            SamReader reader;
            
            if(!reader.Open(filenames[i])) {
                cerr << "Error opening SAM file: " << filenames[i] << endl;
                return -1;
            }

            if(filenames.size() > 1 && i == 0)
                first_header = header;
            
            // TODO: We can probably find a better way to deal with multiple SAM file headers,
            // but for now we should disallow different headers to avoid issues.
            if(i > 0 && header.ToString() != first_header.ToString())
                cerr << "Warning! SAM input files have different headers." << endl;
            
            reader.Close();
        }

        for(int i = 0; i < filenames.size(); i++) {
            SamReader reader;
            
            if(!reader.Open(filenames[i])) {
                cerr << "Error opening SAM file: " << filenames[i] << endl;
                return -1;
            }
            
            header = reader.GetHeader();
            references = reader.GetReferenceData();
            open = true;
            
            if(filenames.size() > 1 && i == 0)
                first_header = header;

            BamAlignment * al = NULL;
            while(true)
            {
                al = reader.GetNextAlignment();
                
                if(NULL == al)
                    break;
                
                putOutputAlignment(al);
            }

            reader.Close();
        }
    } else {
        cerr << "FileReader couldn't detect file format. Aborting." << endl;
        exit(-1);
        return -1;
    }

    return 0;
}
开发者ID:teju85,项目名称:openge,代码行数:100,代码来源:file_reader.cpp

示例11: Run

int MergeTool::Run(int argc, char* argv[]) {

    // parse command line arguments
    Options::Parse(argc, argv, 1);

    // set to default input if none provided
    if ( !m_settings->HasInputBamFilename )
        m_settings->InputFiles.push_back(Options::StandardIn());

    // opens the BAM files (by default without checking for indexes)
    BamMultiReader reader;
    if ( !reader.Open(m_settings->InputFiles, false, true) ) {
        cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl;
        return 1;
    }

    // retrieve header & reference dictionary info
    std::string mergedHeader = reader.GetHeaderText();
    RefVector references = reader.GetReferenceData();

    // open writer
    BamWriter writer;
    bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() && !m_settings->IsForceCompression );
    if ( !writer.Open(m_settings->OutputFilename, mergedHeader, references, writeUncompressed) ) {
        cerr << "ERROR: Could not open BAM file " << m_settings->OutputFilename << " for writing... Aborting." << endl;
        reader.Close();
        return 1;
    }

    // if no region specified, store entire contents of file(s)
    if ( !m_settings->HasRegion ) {
        BamAlignment al;
        while ( reader.GetNextAlignmentCore(al) )
            writer.SaveAlignment(al);
    }

    // otherwise attempt to use region as constraint
    else {

        // if region string parses OK
        BamRegion region;
        if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {

            // attempt to re-open reader with index files
            reader.Close();
            bool openedOK = reader.Open(m_settings->InputFiles, true, true );

            // if error
            if ( !openedOK ) {
                cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl;
                return 1;
            }

            // if index data available, we can use SetRegion
            if ( reader.IsIndexLoaded() ) {

                // attempt to use SetRegion(), if failed report error
                if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
                    cerr << "ERROR: Region requested, but could not set BamReader region to REGION: " << m_settings->Region << " Aborting." << endl;
                    reader.Close();
                    return 1;
                }

                // everything checks out, just iterate through specified region, storing alignments
                BamAlignment al;
                while ( reader.GetNextAlignmentCore(al) )
                    writer.SaveAlignment(al);
            }

            // no index data available, we have to iterate through until we
            // find overlapping alignments
            else {
                BamAlignment al;
                while ( reader.GetNextAlignmentCore(al) ) {
                    if ( (al.RefID >= region.LeftRefID)  && ( (al.Position + al.Length) >= region.LeftPosition ) &&
                            (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
                    {
                        writer.SaveAlignment(al);
                    }
                }
            }
        }

        // error parsing REGION string
        else {
            cerr << "ERROR: Could not parse REGION - " << m_settings->Region << endl;
            cerr << "Be sure REGION is in valid format (see README) and that coordinates are valid for selected references" << endl;
            reader.Close();
            writer.Close();
            return 1;
        }
    }

    // clean & exit
    reader.Close();
    writer.Close();
    return 0;
}
开发者ID:xtmgah,项目名称:TEA,代码行数:98,代码来源:bamtools_merge.cpp


注:本文中的BamMultiReader类示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。