C++ BamReader::CreateIndex方法代码示例

bool BamParse::loadIndex(BamReader& reader)
{
	bool bsignal = reader.OpenIndex(this->filename_index);
	if(bsignal==false) 
	{
		cerr << "Index file not found, now create it!!!"<<endl;
		bool bci=reader.CreateIndex();
		if(bci==false)
		{
			cerr << "Index file cannot be created!!!"<<endl;
			return false;
		}
		else
		{
			bool blct=reader.LocateIndex();
			if(blct==false)
			{
				cerr << "Index file cannot be located!!!"<<endl;
				return false;
			}
		}

	}
	return true;
}

// creates index files for BAM files that don't have them
bool BamMultiReaderPrivate::CreateIndexes(const BamIndex::IndexType& type)
{

    bool errorsEncountered = false;
    m_errorString.clear();

    // iterate over readers
    std::vector<MergeItem>::iterator itemIter = m_readers.begin();
    std::vector<MergeItem>::iterator itemEnd = m_readers.end();
    for (; itemIter != itemEnd; ++itemIter) {
        MergeItem& item = (*itemIter);
        BamReader* reader = item.Reader;
        if (reader == 0) continue;

        // if reader doesn't have an index, create one
        if (!reader->HasIndex()) {
            if (!reader->CreateIndex(type)) {
                m_errorString.append(1, '\t');
                m_errorString.append(reader->GetErrorString());
                m_errorString.append(1, '\n');
                errorsEncountered = true;
            }
        }
    }

    // check for errors encountered before returning success/fail
    if (errorsEncountered) {
        const std::string currentError = m_errorString;
        const std::string message =
            std::string("error while creating index files: \n") + currentError;
        SetErrorString("BamMultiReader::CreateIndexes", message);
        return false;
    } else
        return true;
}

// saves index data to BAM index files (".bai"/".bti") where necessary, returns success/fail
bool BamMultiReader::CreateIndexes(bool useStandardIndex) {
    bool result = true;
    for (vector<pair<BamReader*, BamAlignment*> >::iterator it = readers.begin(); it != readers.end(); ++it) {
        BamReader* reader = it->first;
        result &= reader->CreateIndex(useStandardIndex);
    }
    return result;
}

int IndexTool::Run(int argc, char* argv[]) {
  
    // parse command line arguments
    Options::Parse(argc, argv, 1);
    
    // open our BAM reader
    BamReader reader;
    reader.Open(m_settings->InputBamFilename);
    
    // create index for BAM file
    bool useDefaultIndex = !m_settings->IsUsingBamtoolsIndex;
    reader.CreateIndex(useDefaultIndex);
    
    // clean & exit
    reader.Close();
    return 0;
}

//.........这里部分代码省略.........

    //Check for Reference Fasta sequence
    if (!has_ref)
    {
        cerr << "no FASTA reference provided, cannot realign" << endl;
        exit(1);
    }

    ////Check for reader
    BamReader reader;
    if (STdin == true)
    {
        if (!reader.Open("stdin"))
        {
            cerr << "could not open stdin bam for reading" << endl;
            cerr << reader.GetErrorString() << endl;
            reader.Close();
            printSummary(argv);
        }
    }
    else
    {
        if (has_bamfile == true)
        {
            if (!reader.Open(bamfile))
            {
                cerr << "ERROR: could not open bam files from stdin ... Aborting" << endl;
                cerr << reader.GetErrorString() << endl;
                reader.Close();
                printSummary(argv);
            }

            if ( !reader.LocateIndex() )
                reader.CreateIndex();
        }
        else
        {
            cerr << "--bam flag is set but no bamfile is provided... Aborting" << endl;
            reader.Close();
            printSummary(argv);
        }
    }

    //// Check Region Tags
    if ( (has_regionFile == true) && (has_region == true) )
    {
        cerr << "ERROR: You provide both region and has provide a Set Region List... Aborting" << endl;
        exit(1);
    }

    //// store the names of all the reference sequences in the BAM file
    vector<RefData> referencedata = reader.GetReferenceData();
   
    //// Store Region LIST
    vector<BamRegion> regionlist;
    if (has_region == true)
    {
        BamRegion region;
        ParseRegionString(regionstr, reader, region);
        regionlist.push_back(region);
    }
    else if (has_regionFile == true)
    {
        ifstream RG(RegionFile.c_str(), ios_base::in);
        string line;
        while(getline(RG,line))