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

void testAddHeaderAndTagToFile(const char* inputName, const char* outputName)
{
    SamFile inSam, outSam;
    assert(inSam.OpenForRead(inputName));
    assert(outSam.OpenForWrite(outputName));

    // Read the SAM Header.
    SamFileHeader samHeader;
    assert(inSam.ReadHeader(samHeader));

    // Add a header line.
    assert(samHeader.addHeaderLine("@RG\tID:myID\tSM:mySM") == false);
    assert(samHeader.addHeaderLine("@RG\tID:myID3\tSM:mySM") == true);

    // Write Header
    assert(outSam.WriteHeader(samHeader));

    SamRecord samRecord;
    assert(inSam.ReadRecord(samHeader, samRecord));
    //   validateRead1(samRecord);
    // Add two tags.
    assert(samRecord.addIntTag("XA", 123));
    assert(samRecord.addIntTag("XA", 456));
    assert(samRecord.addTag("RR", 'Z', "myID1"));
    assert(samRecord.addTag("RR", 'Z', "myID2"));

    // Write as Sam.
    assert(outSam.WriteRecord(samHeader, samRecord));

    // TODO, add test to verify it was written correctly.

    // Read a couple of records to make sure it properly can read them even
    // if they are bigger than the original.
    assert(inSam.ReadRecord(samHeader, samRecord));
    assert(inSam.ReadRecord(samHeader, samRecord));

    //  Check the MD tag, which requires the reference.
    GenomeSequence reference("testFiles/chr1_partial.fa");
    assert(SamTags::isMDTagCorrect(samRecord, reference) == false);
    String newMDTag;
    SamTags::createMDTag(newMDTag, samRecord, reference);
    assert(newMDTag == "2T1N0");
    assert(SamTags::updateMDTag(samRecord, reference));
    // Write as Sam.
    assert(outSam.WriteRecord(samHeader, samRecord));
}

//.........这里部分代码省略.........
    // iterator over all @SQ objects
    for(unsigned int i=0; i < numSQ; ++i) {
      pSamHeaderRecord = samHeader.getSQ(fastaFile.vsSequenceNames[i].c_str());
      if ( fastaFile.vsSequenceNames[i].compare(pSamHeaderRecord->getTagValue("SN")) != 0 ) {
	gpLogger->error("SequenceName is not identical between fasta and input BAM file");
      }
      else if ( static_cast<int>(fastaFile.vnSequenceLengths[i]) != atoi(pSamHeaderRecord->getTagValue("LN")) ) {
	gpLogger->error("SequenceLength is not identical between fasta and input BAM file");
      }
      else {
	if ( !sAS.empty() ) 
	  samHeader.setSQTag("AS",sAS.c_str(),fastaFile.vsSequenceNames[i].c_str());
	samHeader.setSQTag("M5",fastaFile.vsMD5sums[i].c_str(),fastaFile.vsSequenceNames[i].c_str());
	if ( !sUR.empty() ) 
	  samHeader.setSQTag("UR",sUR.c_str(),fastaFile.vsSequenceNames[i].c_str());
	if ( !sSP.empty() ) 
	  samHeader.setSQTag("SP",sSP.c_str(),fastaFile.vsSequenceNames[i].c_str());
      }
    }
    gpLogger->write_log("Finished checking the consistency of SQ tags");
  }
  else {
    gpLogger->write_log("Skipped checking the consistency of SQ tags");
  }

  // go over the headers again, 
  // assuming order of HD, SQ, RG, PG, and put proper tags at the end of the original tags

  gpLogger->write_log("Creating the header of new output file");
  //SamFileHeader outHeader;
  samHeader.resetHeaderRecordIter();

  for(unsigned int i=0; i < vsHDHeaders.size(); ++i) {
    samHeader.addHeaderLine(vsHDHeaders[i].c_str());
  }

  /*
  for(int i=0; i < fastaFile.vsSequenceNames.size(); ++i) {
    std::string s("@SQ\tSN:");
    char buf[1024];
    s += fastaFile.vsSequenceNames[i];
    sprintf(buf,"\tLN:%d",fastaFile.vnSequenceLengths[i]);
    s += buf;
    if ( !sAS.empty() ) {
      sprintf(buf,"\tAS:%s",sAS.c_str());
      s += buf;
    }
    if ( !sUR.empty() ) {
      sprintf(buf,"\tUR:%s",sUR.c_str());
      s += buf;
    }
    sprintf(buf,"\tM5:%s",fastaFile.vsMD5sums[i].c_str());
    s += buf;
    if ( !sSP.empty() ) {
      sprintf(buf,"\tSP:%s",sSP.c_str());
      s += buf;
    }
    outHeader.addHeaderLine(s.c_str());
    }*/

  for(unsigned int i=0; i < vsRGHeaders.size(); ++i) {
    samHeader.addHeaderLine(vsRGHeaders[i].c_str());
  }

  for(unsigned int i=0; i < vsPGHeaders.size(); ++i) {
    samHeader.addHeaderLine(vsPGHeaders[i].c_str());

// add readgroup header line to the SamFileHeader
void addReadGroupToHeader(SamFileHeader& header, ReadGroup& rg) {
  if ( !header.addHeaderLine(rg.s_header_line.c_str()) ) {
    Logger::gLogger->error("Failed to add ID = %s, header line %s",rg.s_id.c_str(),rg.s_header_line.c_str());
  }
}