C++ SamRecord::shiftIndelsLeft方法代码示例

//.........这里部分代码省略.........
        refPtr = new GenomeSequence(refFile);
    }

    SamRecord::SequenceTranslation translation;
    if((useBases) && (refPtr != NULL))
    {
        translation = SamRecord::BASES;
    }
    else if((useEquals) && (refPtr != NULL))
    {
        translation = SamRecord::EQUAL;
    }
    else
    {
        useOrigSeq = true;
        translation = SamRecord::NONE;
    }
    
    if(params)
    {
        inputParameters.Status();
    }

    // Open the input file for reading.
    SamFile samIn;
    if(recover) samIn.setAttemptRecovery(true);
    samIn.OpenForRead(inFile);

    // Open the output file for writing.
    SamFile samOut;
    samOut.OpenForWrite(outFile);
    samOut.SetWriteSequenceTranslation(translation);
    samOut.SetReference(refPtr);

    // Read the sam header.
    SamFileHeader samHeader;
    samIn.ReadHeader(samHeader);

    // Write the sam header.
    samOut.WriteHeader(samHeader);

    SamRecord samRecord;

    // Set returnStatus to success.  It will be changed
    // to the failure reason if any of the writes fail.
    SamStatus::Status returnStatus = SamStatus::SUCCESS;

    while(1) {
        try {
            // Keep reading records until ReadRecord returns false.
            while(samIn.ReadRecord(samHeader, samRecord))
            {
                // left shift if necessary.
                if(lshift)
                {
                    samRecord.shiftIndelsLeft();
                }

                // Successfully read a record from the file, so write it.
                if(!samOut.WriteRecord(samHeader, samRecord))
                {
                    // Failed to write a record.
                    fprintf(stderr, "%s\n", samOut.GetStatusMessage());
                    returnStatus = samOut.GetStatus();
                }
            }
            break;
        } catch (std::runtime_error e) {
            std::cerr << "Caught runtime error: " << e.what() << "\n";
            if(!recover) {
                std::cerr << "Corrupted BAM file detected - consider using --recover option.\n";
                break;
            }
            std::cerr << "Attempting to resync at next good BGZF block and BAM record.\n";
            // XXX need to resync SamFile stream here
            bool rc = samIn.attemptRecoverySync(checkSignature, SIGNATURE_LENGTH);
            if(rc) {
                std::cerr << "Successful resync - some data lost.\n";
                continue;    // succeeded
            }
            std::cerr << "Failed to re-sync on data stream.\n";
            break;              // failed to resync
        }
    }

    std::cerr << std::endl << "Number of records read = " << 
        samIn.GetCurrentRecordCount() << std::endl;
    std::cerr << "Number of records written = " << 
        samOut.GetCurrentRecordCount() << std::endl;

    if(refPtr != NULL)
    {
        delete(refPtr);
    }

    // Since the reads were successful, return the status based
    // on the status of the writes.  If any failed, return
    // their failure status.
    return(returnStatus);
}

//.........这里部分代码省略.........
    }
    if(myRefName.Length() != 0 && bed.Length() != 0)
    {
        std::cerr << "Can't specify both refName and bed" << std::endl;
        inputParameters.Status();
        return(-1);
    }

    if(!bed.IsEmpty())
    {
        myBedFile = ifopen(bed, "r");
    }

    if(params)
    {
        inputParameters.Status();
    }

    // Open the file for reading.   
    mySamIn.OpenForRead(inFile);

    // Open the output file for writing.
    SamFile samOut;
    samOut.OpenForWrite(outFile);

    // Open the bam index file for reading if a region was specified.
    if((myRefName.Length() != 0) || (myRefID != UNSET_REF) || (myBedFile != NULL))
    {
        mySamIn.ReadBamIndex(indexFile);
    }

    // Read & write the sam header.
    mySamIn.ReadHeader(mySamHeader);
    samOut.WriteHeader(mySamHeader);

    // Read the sam records.
    SamRecord samRecord;
    // Track the status.
    int numSectionRecords = 0;

    // Set returnStatus to success.  It will be changed
    // to the failure reason if any of the writes fail.
    SamStatus::Status returnStatus = SamStatus::SUCCESS;
        
    while(getNextSection())
    {
        // Keep reading records until they aren't anymore.
        while(mySamIn.ReadRecord(mySamHeader, samRecord))
        {
            if(!readName.IsEmpty())
            {
                // Check for readname.
                if(strcmp(samRecord.getReadName(), readName.c_str()) != 0)
                {
                    // not a matching read name, so continue to the next record.
                    continue;
                }
            }
            
            // Check to see if the read has already been processed.
            if(myPrevEnd != UNSPECIFIED_INT)
            {
                // Because we already know that the bed was sorted, 
                // we know that the previous section started before
                // this one, so if the previous end is greater than
                // this record's end position we know that it
                // was already written in the previous section.
                // Note: can't be equal to the previous end since
                // the end range was exclusive, while
                // get0BasedAlignmentEnd is inclusive.
                // myPrevEnd is reset by getNextSection when a new
                // chromosome is hit.
                if(samRecord.get0BasedAlignmentEnd() < myPrevEnd)
                {
                    // This record was already written.
                    continue;
                }
            }

            // Shift left if applicable.
            if(lshift)
            {
                samRecord.shiftIndelsLeft();
            }

            // Successfully read a record from the file, so write it.
            samOut.WriteRecord(mySamHeader, samRecord);
            ++numSectionRecords;
        }
        myWroteReg = true;
    }

    if(myBedFile != NULL)
    {
        ifclose(myBedFile);
    }
    std::cerr << "Wrote " << outFile << " with " << numSectionRecords
              << " records.\n";
    return(returnStatus);
}