C++ SamFileHeader::getReferenceID方法代码示例

// Get the number of unmapped reads in the specified reference id.  
// Returns -1 for out of range refIDs.
int32_t SamFile::getNumUnMappedReadsFromIndex(const char* refName,
                                              SamFileHeader& header)
{
    // The bam index must have already been read.
    if(myBamIndex == NULL)
    {
        myStatus.setStatus(SamStatus::FAIL_ORDER, 
                           "Cannot get num unmapped reads from the index until it has been read.");
        return(false);
    }
    int32_t refID = BamIndex::REF_ID_UNMAPPED;
    if((strcmp(refName, "") != 0) && (strcmp(refName, "*") != 0))
    {
        // Reference name specified, so read just the "-1" entries.
        refID =  header.getReferenceID(refName);
    }
    return(myBamIndex->getNumUnMappedReads(refID));
}

bool SamFile::processNewSection(SamFileHeader &header)
{
    myNewSection = false;

    // If there is no index file, return failure.
    if(myBamIndex == NULL)
    {
        // No bam index has been read.
        myStatus.setStatus(SamStatus::FAIL_ORDER, 
                           "Cannot read section since there is no index file open");
        throw(std::runtime_error("SOFTWARE BUG: trying to read a BAM record by section prior to opening the BAM Index file."));
        return(false);
    }

    // If there is not a BAM file open for reading, return failure.
    if(!myIsBamOpenForRead)
    {
        // There is not a BAM file open for reading.
        myStatus.setStatus(SamStatus::FAIL_ORDER, 
                           "Cannot read section since there is no bam file open");
        throw(std::runtime_error("SOFTWARE BUG: trying to read a BAM record by section without opening a BAM file."));
        return(false);
    }

    if(myHasHeader == false)
    {
        // The header has not yet been read.
        myStatus.setStatus(SamStatus::FAIL_ORDER, 
                           "Cannot read record since the header has not been read.");
        throw(std::runtime_error("SOFTWARE BUG: trying to read a BAM record by section prior to opening the header."));
        return(false);
    }

    // Indexed Bam open for read, so disable read buffering because iftell
    // will be used.
    // Needs to be done here after we already know that the header has been
    // read.
    myFilePtr->disableBuffering();

    myChunksToRead.clear();
    // Reset the end of the current chunk.  We are resetting our read, so
    // we no longer have a "current chunk" that we are reading.
    myCurrentChunkEnd = 0;

    // Check to see if the read section was set based on the reference name
    // but not yet converted to reference id.
    if(!myRefName.empty())
    {
        myRefID = header.getReferenceID(myRefName.c_str());
        // Clear the myRefName length so this code is only executed once.
        myRefName.clear();

        // Check to see if a reference id was found.
        if(myRefID == SamReferenceInfo::NO_REF_ID)
        {
            myStatus = SamStatus::NO_MORE_RECS;
            return(false);
        }
    }

    // Get the chunks associated with this reference region.
    if(myBamIndex->getChunksForRegion(myRefID, myStartPos, myEndPos, 
                                      myChunksToRead) == true)
    {
        myStatus = SamStatus::SUCCESS;
    }
    else
    {
        String errorMsg = "Failed to get the specified region, refID = ";
        errorMsg += myRefID;
        errorMsg += "; startPos = ";
        errorMsg += myStartPos;
        errorMsg += "; endPos = ";
        errorMsg += myEndPos;
        myStatus.setStatus(SamStatus::FAIL_PARSE, 
                           errorMsg);
    }
    return(true);
}

//.........这里部分代码省略.........
        else if(dbsnpListPtr == NULL)
        {
            std::cerr << "Failed to init the memory allocation for the dbsnpList.\n";
        }
        else
        {
            // Read the dbsnp file.
            StringArray tokens;
            String buffer;
            int position = 0;
            int refID = 0;

            // Loop til the end of the file.
            while (!ifeof(fdbSnp))
            {
                // Read the next line.
                buffer.ReadLine(fdbSnp);
                // If it does not have at least 2 columns, 
                // continue to the next line.
                if (buffer.IsEmpty() || buffer[0] == '#') continue;
                tokens.AddTokens(buffer);
                if(tokens.Length() < 2) continue;

                if(!tokens[1].AsInteger(position))
                {
                    std::cerr << "Improperly formatted region line, start position "
                              << "(2nd column) is not an integer: "
                              << tokens[1]
                              << "; Skipping to the next line.\n";         
                    continue;
                }

                // Look up the reference name.
                refID = samHeader.getReferenceID(tokens[0]);
                if(refID != SamReferenceInfo::NO_REF_ID)
                {
                    // Reference id was found, so add it to the dbsnp
                    dbsnpListPtr->addPosition(refID, position);
                }
        
                tokens.Clear();
                buffer.Clear();
            }
        }
        ifclose(fdbSnp);
    }

    // Read the sam records.
    SamRecord samRecord;

    int numReads = 0;

    //////////////////////
    // Setup in case doing a quality count.
    // Quality histogram.
    const int MAX_QUAL = 126;
    const int START_QUAL = 33;
    uint64_t qualCount[MAX_QUAL+1];
    for(int i = 0; i <= MAX_QUAL; i++)
    {
        qualCount[i] = 0;
    }
    
    const int START_PHRED = 0;
    const int PHRED_DIFF = START_QUAL - START_PHRED;
    const int MAX_PHRED = MAX_QUAL - PHRED_DIFF;