C++ SamFile::ReadRecord方法代码示例

void testRead(SamFile &inSam)
{
    // Read the SAM Header.
    SamFileHeader samHeader;
    assert(inSam.ReadHeader(samHeader));

    validateHeader(samHeader);

    testCopyHeader(samHeader);    

    testModHeader(samHeader);

    SamRecord samRecord;
    assert(inSam.ReadRecord(samHeader, samRecord) == true);
    validateRead1(samRecord);

    // Set a new quality and get the buffer.
    samRecord.setQuality("ABCDE");
    validateRead1ModQuality(samRecord);
    //   void* buffer = samRecord.getRecordBuffer();

    assert(inSam.ReadRecord(samHeader, samRecord) == true);
    validateRead2(samRecord);

    assert(inSam.ReadRecord(samHeader, samRecord) == true);
    validateRead3(samRecord);

    assert(inSam.ReadRecord(samHeader, samRecord) == true);
    validateRead4(samRecord);

    assert(inSam.ReadRecord(samHeader, samRecord) == true);
    validateRead5(samRecord);

    assert(inSam.ReadRecord(samHeader, samRecord) == true);
    validateRead6(samRecord);

    assert(inSam.ReadRecord(samHeader, samRecord) == true);
    validateRead7(samRecord);

    assert(inSam.ReadRecord(samHeader, samRecord) == true);
    validateRead8(samRecord);

    assert(inSam.ReadRecord(samHeader, samRecord) == true);
    validateRead9(samRecord);

    assert(inSam.ReadRecord(samHeader, samRecord) == true);
    validateRead10(samRecord);
}

void GenomeRegionSeqStats::CalcClusters(String &bamFile, int minMapQuality)
{
  SamFile sam;
  SamRecord samRecord;
  SamFileHeader samHeader;

  if(!sam.OpenForRead(bamFile.c_str()))
    error("Open BAM file %s failed!\n", bamFile.c_str());

  if(!sam.ReadHeader(samHeader)) {
      error("Read BAM file header %s failed!\n", bamFile.c_str());
  }
  
  if(depth.size()==0) depth.resize(referencegenome.sequenceLength());
  
  String contigLabel;
  uint32_t start;
  uint32_t gstart;
  Reset();
  while(sam.ReadRecord(samHeader, samRecord))
    {
      nReads++;
      if(samRecord.getFlag() & SamFlag::UNMAPPED) nUnMapped++;

      if(samRecord.getMapQuality() < minMapQuality) continue;

      CigarRoller cigar(samRecord.getCigar());

      int nonClipSequence = 0;

      if(cigar.size()!=0 && cigar[0].operation==Cigar::softClip)
          nonClipSequence = cigar[0].count;

      contigLabel = samRecord.getReferenceName();
      start = nonClipSequence + samRecord.get0BasedPosition();  // start is 0-based

      gstart = referencegenome.getGenomePosition(contigLabel.c_str(), start);

      if(IsInRegions(contigLabel, start, start+samRecord.getReadLength())) continue;

      for(uint32_t i=gstart; i<gstart+samRecord.getReadLength(); i++)
       if(depth[i]<MAXDP)
        depth[i]++;
      nMappedOutTargets++;
    }
}

void GenomeRegionSeqStats::CalcRegionStats(String &bamFile)
{
  SamFile sam;
  SamRecord samRecord;
  SamFileHeader samHeader;

  if(!sam.OpenForRead(bamFile.c_str()))
    error("Open BAM file %s failed!\n", bamFile.c_str());

  if(!sam.ReadHeader(samHeader)) {
      error("Read BAM file header %s failed!\n", bamFile.c_str());
  }
  
  String contigLabel;
  int start, end;
  Reset();
  while(sam.ReadRecord(samHeader, samRecord))
    {
      nReads++;
      if(samRecord.getFlag() & SamFlag::UNMAPPED) nUnMapped++;

      if(contigFinishedCnt>=contigs.size()) continue;

      CigarRoller cigar(samRecord.getCigar());

      int nonClipSequence = 0;

      if(cigar.size()!=0 && cigar[0].operation==Cigar::softClip)
          nonClipSequence = cigar[0].count;

      contigLabel = samRecord.getReferenceName();
      start = nonClipSequence + samRecord.get0BasedPosition();  // start is 0-based
      end = start + samRecord.getReadLength() - 1;
      if(UpdateRegionStats(contigLabel, start, end)) nMapped2Targets++;
    }
    CalcRegionReadCountInGCBins();
    CalcGroupReadCountInGCBins();
    std::cout << "Total reads : " << nReads << std::endl;
}

SamStatus::Status ClipOverlap::readCoordRecord(SamFile& samIn,
                                               SamRecord** recordPtr, 
                                               MateMapByCoord& mateMap,
                                               SamCoordOutput* outputBufferPtr)
{
    // Null pointer, so get a new pointer.
    if(*recordPtr == NULL)
    {
        *recordPtr = myPool.getRecord();
        if(*recordPtr == NULL)
        {
            // Failed to allocate a new record.
            // Try to free up records from the mate map
            if(!forceRecordFlush(mateMap, outputBufferPtr))
            {
                std::cerr << "Failed to flush the output buffer.\n";
                return(SamStatus::FAIL_IO);
            }
            // Try to get a new record, one should have been cleared.
            *recordPtr = myPool.getRecord();
            if(*recordPtr == NULL)
            {
                std::cerr << "Failed to allocate any records.\n";
                return(SamStatus::FAIL_MEM);
            }
        }
    }

    // RecordPtr is set.
    if(!samIn.ReadRecord(mySamHeader, **recordPtr))
    {
        // Nothing to process, so return.
        return(samIn.GetStatus());
    }
    return(SamStatus::SUCCESS);
}

//.........这里部分代码省略.........
        if(myFirstFile == NULL)
        {
            std::cerr << "Failed to open " << firstOut
                      << " so can't convert bam2FastQ.\n";
            return(-1);
        }
        if(mySecondFile == NULL)
        {
            std::cerr << "Failed to open " << secondOut
                      << " so can't convert bam2FastQ.\n";
            return(-1);
        }
    }

    if((readName) || (strcmp(mySamHeader.getSortOrder(), "queryname") == 0))
    {
        readName = true;
    }
    else
    {
        // defaulting to coordinate sorted.
        samIn.setSortedValidation(SamFile::COORDINATE);
    }

    // Setup the '=' translation if the reference was specified.
    if(!refFile.IsEmpty())
    {
        GenomeSequence* refPtr = new GenomeSequence(refFile);
        samIn.SetReadSequenceTranslation(SamRecord::BASES);
        samIn.SetReference(refPtr);
    }

    SamRecord* recordPtr;
    int16_t samFlag;

    SamStatus::Status returnStatus = SamStatus::SUCCESS;
    while(returnStatus == SamStatus::SUCCESS)
    {
        recordPtr = myPool.getRecord();
        if(recordPtr == NULL)
        {
            // Failed to allocate a new record.
            throw(std::runtime_error("Failed to allocate a new SAM/BAM record"));
        }
        if(!samIn.ReadRecord(mySamHeader, *recordPtr))
        {
            // Failed to read a record.
            returnStatus = samIn.GetStatus();
            continue;
        }

        // Have a record.  Check to see if it is a pair or unpaired read.
        samFlag = recordPtr->getFlag();
        if(SamFlag::isPaired(samFlag))
        {
            if(readName)
            {
                handlePairedRN(*recordPtr);
            }
            else
            {
                handlePairedCoord(*recordPtr);
            }
        }
        else
        {
            ++myNumUnpaired;
            writeFastQ(*recordPtr, myUnpairedFile,
                       myUnpairedFileNameExt);
        }
    }

    // Flush All
    cleanUpMateMap(0, true);

    if(returnStatus == SamStatus::NO_MORE_RECS)
    {
        returnStatus = SamStatus::SUCCESS;
    }

    samIn.Close();
    closeFiles();
    
    // Output the results
    std::cerr << "\nFound " << myNumPairs << " read pairs.\n";
    std::cerr << "Found " << myNumUnpaired << " unpaired reads.\n";
    if(myNumMateFailures != 0)
    {
        std::cerr << "Failed to find mates for " << myNumMateFailures
                  << " reads, so they were written as unpaired\n"
                  << "  (not included in either of the above counts).\n";
    }
    if(myNumQualTagErrors != 0)
    {
        std::cerr << myNumQualTagErrors << " records did not have tag "
                  << myQField.c_str() << " or it was invalid, so the quality field was used for those records.\n";
    }

    return(returnStatus);
}

//.........这里部分代码省略.........
      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());
  }

  samOut.WriteHeader(samHeader);
  gpLogger->write_log("Adding %d HD, %d RG, and %d PG headers",vsHDHeaders.size(), vsRGHeaders.size(), vsPGHeaders.size());
  gpLogger->write_log("Finished writing output headers");

  // parse RG tag and get RG ID to append
  std::string sRGID;
  if ( ! vsRGHeaders.empty() ) {
    std::vector<std::string> tokens;
    FastaFile::tokenizeString( vsRGHeaders[0].c_str(), tokens );
    for(unsigned int i=0; i < tokens.size(); ++i) {
      if ( tokens[i].find("ID:") == 0 ) {
	sRGID = tokens[i].substr(3);
      }
    }
  }
  
  gpLogger->write_log("Writing output BAM file");
  SamRecord samRecord;
  while (samIn.ReadRecord(samHeader, samRecord) == true) {
    if ( !sRGID.empty() ) {
      if ( samRecord.addTag("RG",'Z',sRGID.c_str()) == false ) {
	gpLogger->error("Failed to add a RG tag %s",sRGID.c_str());
      }
      // temporary code added
      if ( strncmp(samRecord.getReadName(),"seqcore_",8) == 0 ) {
	char buf[1024];
	sprintf(buf,"UM%s",samRecord.getReadName()+8);
	samRecord.setReadName(buf);
      }
    }
    samOut.WriteRecord(samHeader, samRecord);
    //if ( samIn.GetCurrentRecordCount() == 1000 ) break;
  }
  samOut.Close();
  gpLogger->write_log("Successfully written %d records",samIn.GetCurrentRecordCount());
  delete gpLogger;
  return 0;
}

SamStatus::Status ClipOverlap::handleSortedByReadName(SamFile& samIn, 
                                                      SamFile* samOutPtr)
{
    // Set returnStatus to success.  It will be changed
    // to the failure reason if any of the writes fail.
    SamStatus::Status returnStatus = SamStatus::SUCCESS;

    // Read the sam records.
    SamRecord* prevSamRecord = NULL;
    SamRecord* samRecord = new SamRecord;
    SamRecord* tmpRecord = new SamRecord;
    if((samRecord == NULL) || (tmpRecord == NULL))
    {
        std::cerr << "Failed to allocate a SamRecord, so exit.\n";
        return(SamStatus::FAIL_MEM);
    }

    // Keep reading records until ReadRecord returns false.
    while(samIn.ReadRecord(mySamHeader, *samRecord))
    {
        int16_t flag = samRecord->getFlag();
        if((flag & myIntExcludeFlags) != 0)
        {
            // This read should not be checked for overlaps.

            // Check if there is a previous SamRecord.
            if(prevSamRecord != NULL)
            {
                // There is a previous record.
                // If it has a different read name, write it.
                if(strcmp(samRecord->getReadName(), 
                          prevSamRecord->getReadName()) != 0)
                {
                    // Different read name, so write the previous record.
                    if((samOutPtr != NULL) && !myOverlapsOnly)
                    {
                        if(!samOutPtr->WriteRecord(mySamHeader, *prevSamRecord))
                        {
                            // Failed to write a record.
                            fprintf(stderr, "%s\n", samOutPtr->GetStatusMessage());
                            returnStatus = samOutPtr->GetStatus();
                        }
                    }
                    // Clear the previous record info.
                    tmpRecord = prevSamRecord;
                    prevSamRecord = NULL;
                } 
                // If it has the same read name, leave it in case there is another read with that name
            }
            // This record is not being checked for overlaps, so just write it and continue
            if((samOutPtr != NULL) && !myOverlapsOnly)
            {
                if(!samOutPtr->WriteRecord(mySamHeader, *samRecord))
                {
                    // Failed to write a record.
                    fprintf(stderr, "%s\n", samOutPtr->GetStatusMessage());
                    returnStatus = samOutPtr->GetStatus();
                }
            }
            continue;
        }

        if(prevSamRecord == NULL)
        {
            // Nothing to compare this record to, so set this
            // record to the previous, and the next record.
            prevSamRecord = samRecord;
            samRecord = tmpRecord;
            tmpRecord = NULL;
            continue;
        }

        // Check if the read name matches the previous read name.
        if(strcmp(samRecord->getReadName(), 
                  prevSamRecord->getReadName()) == 0)
        {
            bool overlap = false;
            // Same Read Name, so check clipping.
            OverlapHandler::OverlapInfo prevClipInfo = 
                myOverlapHandler->getOverlapInfo(*prevSamRecord);
            OverlapHandler::OverlapInfo curClipInfo = 
                myOverlapHandler->getOverlapInfo(*samRecord);
            
            // If either indicate a complete clipping, clip both.
            if((prevClipInfo == OverlapHandler::NO_OVERLAP_WRONG_ORIENT) ||
               (curClipInfo == OverlapHandler::NO_OVERLAP_WRONG_ORIENT))
            {
                overlap = true;
                myOverlapHandler->handleNoOverlapWrongOrientation(*prevSamRecord);
                // Don't update stats since this is the 2nd in the pair
                myOverlapHandler->handleNoOverlapWrongOrientation(*samRecord, 
                                                                  false);
            }
            else if((prevClipInfo == OverlapHandler::OVERLAP) ||
                    (prevClipInfo == OverlapHandler::SAME_START))
            {
                // The previous read starts at or before the current one.
                overlap = true;
                myOverlapHandler->handleOverlapPair(*prevSamRecord,
                                                    *samRecord);
//.........这里部分代码省略.........

void testIndex(BamIndex& bamIndex)
{
    assert(bamIndex.getNumMappedReads(1) == 2);
    assert(bamIndex.getNumUnMappedReads(1) == 0);
    assert(bamIndex.getNumMappedReads(0) == 4);
    assert(bamIndex.getNumUnMappedReads(0) == 1);
    assert(bamIndex.getNumMappedReads(23) == -1);
    assert(bamIndex.getNumUnMappedReads(23) == -1);
    assert(bamIndex.getNumMappedReads(-1) == 0);
    assert(bamIndex.getNumUnMappedReads(-1) == 2);
    assert(bamIndex.getNumMappedReads(-2) == -1);
    assert(bamIndex.getNumUnMappedReads(-2) == -1);
    assert(bamIndex.getNumMappedReads(22) == 0);
    assert(bamIndex.getNumUnMappedReads(22) == 0);

    // Get the chunks for reference id 1.
    Chunk testChunk;
    SortedChunkList chunkList;
    assert(bamIndex.getChunksForRegion(1, -1, -1, chunkList) == true);
    assert(!chunkList.empty());
    testChunk = chunkList.pop();
    assert(chunkList.empty());
    assert(testChunk.chunk_beg == 0x4e7);
    assert(testChunk.chunk_end == 0x599);

    // Get the chunks for reference id 0.
    assert(bamIndex.getChunksForRegion(0, -1, -1, chunkList) == true);
    assert(!chunkList.empty());
    testChunk = chunkList.pop();
    assert(chunkList.empty());
    assert(testChunk.chunk_beg == 0x360);
    assert(testChunk.chunk_end == 0x4e7);


    // Get the chunks for reference id 2.
    assert(bamIndex.getChunksForRegion(2, -1, -1, chunkList) == true);
    assert(!chunkList.empty());
    testChunk = chunkList.pop();
    assert(chunkList.empty());
    assert(testChunk.chunk_beg == 0x599);
    assert(testChunk.chunk_end == 0x5ea);

    // Get the chunks for reference id 3.
    // There isn't one for this ref id, but still successfully read the file,
    // so it should return true, but the list should be empty.
    assert(bamIndex.getChunksForRegion(3, -1, -1, chunkList) == true);
    assert(chunkList.empty());

    // Test reading an indexed bam file.
    SamFile inFile;
    assert(inFile.OpenForRead("testFiles/sortedBam.bam"));
    inFile.setSortedValidation(SamFile::COORDINATE);
    assert(inFile.ReadBamIndex("testFiles/sortedBam.bam.bai"));
    SamFileHeader samHeader;
    assert(inFile.ReadHeader(samHeader));
    SamRecord samRecord;

    // Test getting num mapped/unmapped reads.
    assert(inFile.getNumMappedReadsFromIndex(1) == 2);
    assert(inFile.getNumUnMappedReadsFromIndex(1) == 0);
    assert(inFile.getNumMappedReadsFromIndex(0) == 4);
    assert(inFile.getNumUnMappedReadsFromIndex(0) == 1);
    assert(inFile.getNumMappedReadsFromIndex(23) == -1);
    assert(inFile.getNumUnMappedReadsFromIndex(23) == -1);
    assert(inFile.getNumMappedReadsFromIndex(-1) == 0);
    assert(inFile.getNumUnMappedReadsFromIndex(-1) == 2);
    assert(inFile.getNumMappedReadsFromIndex(-2) == -1);
    assert(inFile.getNumUnMappedReadsFromIndex(-2) == -1);
    assert(inFile.getNumMappedReadsFromIndex(22) == 0);
    assert(inFile.getNumUnMappedReadsFromIndex(22) == 0);

    assert(inFile.getNumMappedReadsFromIndex("2", samHeader) == 2);
    assert(inFile.getNumUnMappedReadsFromIndex("2", samHeader) == 0);
    assert(inFile.getNumMappedReadsFromIndex("1", samHeader) == 4);
    assert(inFile.getNumUnMappedReadsFromIndex("1", samHeader) == 1);
    assert(inFile.getNumMappedReadsFromIndex("22", samHeader) == 0);
    assert(inFile.getNumUnMappedReadsFromIndex("22", samHeader) == 0);
    assert(inFile.getNumMappedReadsFromIndex("", samHeader) == 0);
    assert(inFile.getNumUnMappedReadsFromIndex("*", samHeader) == 2);
    assert(inFile.getNumMappedReadsFromIndex("unknown", samHeader) == -1);
    assert(inFile.getNumUnMappedReadsFromIndex("unknown", samHeader) == -1);
    assert(inFile.getNumMappedReadsFromIndex("X", samHeader) == 0);
    assert(inFile.getNumUnMappedReadsFromIndex("X", samHeader) == 0);

    // Section -1 = Ref *: 2 records (8 & 10 from testSam.sam that is reflected
    // in the validation.
    assert(inFile.SetReadSection(-1));
    assert(inFile.ReadRecord(samHeader, samRecord));
    validateRead8(samRecord);
    assert(inFile.ReadRecord(samHeader, samRecord));
    validateRead10(samRecord);
    assert(inFile.ReadRecord(samHeader, samRecord) == false);

    // Section 2 = Ref 3: 1 records (9 from testSam.sam that is reflected
    // in the validation.
    assert(inFile.SetReadSection(2));
    assert(inFile.ReadRecord(samHeader, samRecord));
    validateRead9(samRecord);
    assert(inFile.ReadRecord(samHeader, samRecord) == false);

//.........这里部分代码省略.........

/*
	if a discordant read is mapped to MEI (overlap with MEI coord)
		add centor of ( anchor_end + 3*avr_ins_var )
	skip unmap & clip
	check 3 types at the same time
*/
void Sites::AddDiscoverSiteFromSingleBam( SingleSampleInfo & si )
{
/*for(int i=0;i<NMEI; i++) {
std::cout << "m=" << i << ": ";
for(map<string, map<int, bool> >::iterator t=meiCoord[m].begin(); t!=meiCoord[m].end(); t++)
std::cout << t->first << "->" << t->second.size() << " ";
std::cout << std::endl;
}*/

	avr_read_length = si.avr_read_length;
	avr_ins_size = si.avr_ins_size;
	min_read_length = avr_read_length / 3;
	current_depth = si.depth;
//	total_depth += current_depth;

	resetDepthAddFlag();
	
	SamFile bam;
	SamFileHeader bam_header;
	OpenBamAndBai( bam,bam_header, si.bam_name );
	for( int i=0; i<pchr_list->size(); i++ ) {
		string chr = (*pchr_list)[i];
//		if ( !single_chr.empty() && chr.compare(single_chr)!=0 )
//			continue;
		if ( siteList.find(chr) == siteList.end() )
			siteList[chr].clear();
//		map<string, map<int, SingleSite> >::iterator pchr = siteList[m].find(chr);
//		map<string, map<int, bool> >::iterator coord_chr_ptr = meiCoord[m].find(chr);
//		if (coord_chr_ptr == meiCoord[m].end())
//			continue;
		bool section_status;
		if (range_start<0) { // no range
			section_status = bam.SetReadSection( chr.c_str() );
			if (!section_status) {
				string str = "Cannot set read section at chr " + chr;
				morphWarning( str );
			}
		}
		else { // set range
			section_status = bam.SetReadSection( chr.c_str(), range_start, range_end );
			if (!section_status) {
				string str = "Cannot set read section at chr " + chr + " " + std::to_string(range_start) + "-" + std::to_string(range_end); 
				morphWarning( str );
			}			
		}
		
		// DO ADDING
//		if (siteList[chr].empty())
//			p_reach_last = 1;
//		else {
//			p_reach_last = 0;
		pnearest = siteList[chr].begin();
//		}
		SingleSite new_site; // temporary cluster. will be added to map later.
		new_site.depth = current_depth;
		bool start_new = 1; // check if need to add new_site to map and start new new_site
		SamRecord rec;
		int between = 0; // count #reads after new_site.end. If end changed, add it to rcount and reset to zero
		while( bam.ReadRecord( bam_header, rec ) ) {
			if (!start_new) {
				if (rec.get1BasedPosition() >= new_site.end)
					between++;
				else
					new_site.rcount++;
			}
			if (rec.getFlag() & 0x2)
				continue;
			if ( OneEndUnmap( rec.getFlag() ) )
				continue;
			if ( IsSupplementary(rec.getFlag()) )
				continue;
			if ( rec.getReadLength() < min_read_length )
				continue;
			if ( rec.getMapQuality() < MIN_QUALITY )
				continue;
			if (chr.compare(rec.getMateReferenceName())==0 && rec.getInsertSize() < abs(avr_ins_size*2))
				continue;
			bool is_mei = 0;
			vector<bool> is_in_coord;
			is_in_coord.resize(3, 0);
			for(int m=0; m<NMEI; m++) {
				map<string, map<int, bool> >::iterator coord_chr_ptr = meiCoord[m].find(rec.getMateReferenceName());
				if (coord_chr_ptr == meiCoord[m].end())
					is_in_coord[m] = 0;
				else
					is_in_coord[m] = isWithinCoord( rec.get1BasedMatePosition(), coord_chr_ptr->second ); // within MEI coord
				if (is_in_coord[m])
					is_mei = 1;
			}
			if (!is_mei)
				continue;
			if (start_new) {
				setNewCluster( is_in_coord, new_site,rec);
				start_new = 0;
//.........这里部分代码省略.........

void setReadCountInSection( vector<int> & raw_counts, string & chr, int center, SamFile & samIn, SamFileHeader & samHeader, vector<RefSeq*> & REF_SEQ )
{
	int st = center - WIN/2;
	int ed = center + WIN/2;
	bool section_status = samIn.SetReadSection( chr.c_str(), st, ed );
	if (!section_status) {
		std::cerr << "Warning: Unable to set read section: " << chr << ": " << st << "-" << ed << ". Set section depth = 0!" << std::endl;
		return;
	}

// proper reads	
	map<string, vector< DiscPair > > disc_recs; // record where the disc come from
	ProperDeck pDeck( REF_SEQ );
	SamRecord sam_rec;
	while( samIn.ReadRecord(samHeader, sam_rec) ) {
		bool pass_qc = PassQC( sam_rec );
		if ( !pass_qc )
			continue;
		if ( sam_rec.getFlag() & 0x2 ) {
			if ( sam_rec.getInsertSize() > 0 )
				pDeck.Add( sam_rec );
			else {
				RetrievedIndex rv = pDeck.RetrieveIndex( sam_rec );
				int index = getRetrievedIndexToRawCounts( rv );
				if (index >= 0) { // for read partially in window, only add clip
					if ( sam_rec.get1BasedPosition() < st || sam_rec.get1BasedAlignmentEnd() > ed ) {
						if ( index >= 2 )
							raw_counts[ index ]++;
					}
					else
						raw_counts[ index ]++;
				}
			}
		}
		else { // disc: rec info and wait to reset section later
			if ( sam_rec.getReadLength() < 30 )
				continue;
			string mate_chr = sam_rec.getMateReferenceName();
		// check if this one is valid as anchor
			DiscPair new_pair( 1, 0, sam_rec, REF_SEQ );
			disc_recs[mate_chr].push_back( new_pair );
		}
	}
	
// disc reads
	for( map<string, vector< DiscPair > >::iterator chr_it = disc_recs.begin(); chr_it != disc_recs.end(); chr_it++ ) {
		for( vector< DiscPair >::iterator dp_it = chr_it->second.begin(); dp_it != chr_it->second.end(); dp_it++ ) {
			bool section_status = samIn.SetReadSection( chr_it->first.c_str(), dp_it->GetSecondAlignPosition(), dp_it->GetSecondAlignPosition() + WIN );
			if (!section_status) {
				std::cerr << "ERROR: Unable to set read section: " << chr << ": " << st << "-" << ed << std::endl;
				exit(1);
			}
			SamRecord sam_rec;
			while( samIn.ReadRecord(samHeader, sam_rec) ) {
				bool pass_qc = PassQC( sam_rec );
				if ( !pass_qc )
					continue;
				if ( !DiscSamPass(sam_rec) )
					continue;
				int position = sam_rec.get1BasedPosition();
				if ( position > dp_it->GetFirstAlignPosition() )
					break;
				if ( sam_rec.getFlag() & 0x2 )
					continue;
				bool same_pair = dp_it->IsSamePair( sam_rec );
				if ( !same_pair )
					continue;
			// now add ro raw stats: always use first as anchor
				dp_it->AddSecondToPair( sam_rec );
				Loci loci = dp_it->GetFirstLoci();
				if ( dp_it->FirstValid() ) {
					int index = getLociToRawCounts( loci );
					raw_counts[ index ]++;
				// clear & break
					break;		
				}
			}
		}
	}		
}

void testFlagRead(const char* fileName)
{
    SamFile inSam;
    SamFileHeader samHeader;
    SamRecord samRecord;

    ////////////////////////////////////////////////////////////
    // Required flag 0x48  (only flag 73 matches)
    // Exclude nothing
    assert(inSam.OpenForRead(fileName));
    assert(inSam.ReadHeader(samHeader));
    validateHeader(samHeader);
    inSam.SetReadFlags(0x48, 0x0);

    assert(inSam.ReadRecord(samHeader, samRecord) == true);
    validateRead1(samRecord);

    assert(inSam.ReadRecord(samHeader, samRecord) == false);

    inSam.Close();

    ////////////////////////////////////////////////////////////
    // No required flags.
    // Exclude 0x48.  This leaves just the one read with flag 133.
    assert(inSam.OpenForRead(fileName));
    assert(inSam.ReadHeader(samHeader));
    validateHeader(samHeader);
    inSam.SetReadFlags(0x0, 0x48);

    assert(inSam.ReadRecord(samHeader, samRecord) == true);
    validateRead2(samRecord);

    assert(inSam.ReadRecord(samHeader, samRecord) == false);

    inSam.Close();

    ////////////////////////////////////////////////////////////
    // Required flag 0x40 
    // Exclude 0x48.
    // This will not find any records since the exclude and required conflict.
    assert(inSam.OpenForRead(fileName));
    assert(inSam.ReadHeader(samHeader));
    validateHeader(samHeader);
    inSam.SetReadFlags(0x40, 0x48);

    assert(inSam.ReadRecord(samHeader, samRecord) == false);

    inSam.Close();

    ////////////////////////////////////////////////////////////
    // Required flag 0x4
    // Exclude 0x8.
    // Only finds flag 133.
    assert(inSam.OpenForRead(fileName));
    assert(inSam.ReadHeader(samHeader));
    validateHeader(samHeader);
    inSam.SetReadFlags(0x4, 0x8);

    assert(inSam.ReadRecord(samHeader, samRecord) == true);
    validateRead2(samRecord);

    assert(inSam.ReadRecord(samHeader, samRecord) == false);

    inSam.Close();

     ////////////////////////////////////////////////////////////
    // Required flag 0x4
    // Exclude nothing
    // Finds flags 133 & 141.
    assert(inSam.OpenForRead(fileName));
    assert(inSam.ReadHeader(samHeader));
    validateHeader(samHeader);
    inSam.SetReadFlags(0x4, 0x0);

    assert(inSam.ReadRecord(samHeader, samRecord) == true);
    validateRead2(samRecord);

    assert(inSam.ReadRecord(samHeader, samRecord) == true);
    validateRead8(samRecord);

    assert(inSam.ReadRecord(samHeader, samRecord) == true);
    validateRead10(samRecord);

    assert(inSam.ReadRecord(samHeader, samRecord) == false);

    inSam.Close();
}

//.........这里部分代码省略.........
                  numTrimBaseL);
      }
      else
      {
          // ignore strand, treating forward & reverse strands the same
          fprintf(stderr,"\t#Bases to trim from the left of reverse strands : %d\n",
                  numTrimBaseL);
          fprintf(stderr,"\t#Bases to trim from the right of reverse strands : %d\n",
                  numTrimBaseR);
      }
  }
 
   // Read the sam header.
   SamFileHeader samHeader;
   if(!samIn.ReadHeader(samHeader))
   {
      fprintf(stderr, "%s\n", samIn.GetStatusMessage());
      return(samIn.GetStatus());
   }

   // Write the sam header.
   if(!samOut.WriteHeader(samHeader))
   {
      fprintf(stderr, "%s\n", samOut.GetStatusMessage());
      return(samOut.GetStatus());     
   }

   SamRecord samRecord;
   char seq[65536];
   char qual[65536];
   int i, len;

   // Keep reading records until ReadRecord returns false.
   while(samIn.ReadRecord(samHeader, samRecord)) {
     // Successfully read a record from the file, so write it.
     strcpy(seq,samRecord.getSequence());
     strcpy(qual,samRecord.getQuality());

     // Number of bases to trim from the left/right,
     // set based on ignoreStrand flag and strand info.
     int trimLeft = numTrimBaseL;
     int trimRight = numTrimBaseR;
     if(!ignoreStrand)
     {
         if(SamFlag::isReverse(samRecord.getFlag()))
         {
             // We are reversing the reverse reads,
             // so swap the left & right trim counts.
             trimRight = numTrimBaseL;
             trimLeft = numTrimBaseR;
         }
     }

     len = strlen(seq);
     // Do not trim if sequence is '*'
     if ( strcmp(seq, "*") != 0 ) {
       bool qualValue = true;
       if(strcmp(qual, "*") == 0)
       {
           qualValue = false;
       }
       int qualLen = strlen(qual);
       if ( (qualLen != len) && qualValue ) {
         fprintf(stderr,"ERROR: Sequence and Quality have different length\n");
         return(-1);
       }

int GapInfo::processFile(const char* inputFileName, const char* outputFileName,
                         const char* refFile, bool detailed,
                         bool checkFirst, bool checkStrand)
{
    // Open the file for reading.
    SamFile samIn;
    samIn.OpenForRead(inputFileName);

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

    SamRecord samRecord;

    GenomeSequence* refPtr = NULL;
    if(strcmp(refFile, "") != 0)
    {
        refPtr = new GenomeSequence(refFile);
    }

    IFILE outFile = ifopen(outputFileName, "w");

    // Map for summary.
    std::map<int, int> gapInfoMap;


    // Keep reading records until ReadRecord returns false.
    while(samIn.ReadRecord(samHeader, samRecord))
    {
        uint16_t samFlags = samRecord.getFlag();

        if((!SamFlag::isMapped(samFlags)) || 
           (!SamFlag::isMateMapped(samFlags)) ||
           (!SamFlag::isPaired(samFlags)) ||
           (samFlags & SamFlag::SECONDARY_ALIGNMENT) || 
           (SamFlag::isDuplicate(samFlags)) ||
           (SamFlag::isQCFailure(samFlags)))
        {
            // unmapped, mate unmapped, not paired,
            // not the primary alignment,
            // duplicate, fails vendor quality check 
            continue;
        }

        // No gap info if the chromosome names are different or
        // are unknown.
        int32_t refID = samRecord.getReferenceID();
        if((refID != samRecord.getMateReferenceID()) || (refID == -1))
        {
            continue;
        }

        int32_t readStart = samRecord.get0BasedPosition();
        int32_t mateStart = samRecord.get0BasedMatePosition();

        // If the mate starts first, then the pair was processed by
        // the mate.
        if(mateStart < readStart)
        {
            continue;
        }
        if((mateStart == readStart) && (SamFlag::isReverse(samFlags)))
        {
            // read and mate start at the same position, so 
            // only process the forward strand.
            continue;
        }

        // Process this read pair.
        int32_t readEnd = samRecord.get0BasedAlignmentEnd();
        
        int32_t gapSize = mateStart - readEnd - 1;

        if(detailed)
        {
            // Output the gap info.
            ifprintf(outFile, "%s\t%d\t%d", 
                     samRecord.getReferenceName(), readEnd+1, gapSize);
            
            // Check if it is not the first or if it is not the forward strand.
            if(checkFirst && !SamFlag::isFirstFragment(samFlags))
            {
                ifprintf(outFile, "\tNotFirst");
            }
            if(checkStrand && SamFlag::isReverse(samFlags))
            {
                ifprintf(outFile, "\tReverse");
            }
            ifprintf(outFile, "\n");
        }
        else
        {
            // Summary.
            // Skip reads that are not the forward strand.
            if(SamFlag::isReverse(samFlags))
            {
                // continue
                continue;
            }

//.........这里部分代码省略.........

//.........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.........
    //////////////////////
    // 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;
    uint64_t phredCount[MAX_PHRED+1];
    for(int i = 0; i <= MAX_PHRED; i++)
    {
        phredCount[i] = 0;
    }
    
    int refPos = 0;
    Cigar* cigarPtr = NULL;
    char cigarChar = '?';
    // Exclude clips from the qual/phred counts if unmapped reads are excluded.
    bool qualExcludeClips = excludeFlags & SamFlag::UNMAPPED;

    //////////////////////////////////
    // When not reading by sections, getNextSection returns true
    // the first time, then false the next time.
    while(getNextSection(samIn))
    {
        // Keep reading records from the file until SamFile::ReadRecord
        // indicates to stop (returns false).
        while(((maxNumReads < 0) || (numReads < maxNumReads)) && samIn.ReadRecord(samHeader, samRecord))
        {
            // Another record was read, so increment the number of reads.
            ++numReads;
            // See if the quality histogram should be genereated.
            if(qual || phred)
            {
                // Get the quality.
                const char* qual = samRecord.getQuality();
                // Check for no quality ('*').
                if((qual[0] == '*') && (qual[1] == 0))
                {
                    // This record does not have a quality string, so no 
                    // quality processing is necessary.
                }
                else
                {
                    int index = 0;
                    cigarPtr = samRecord.getCigarInfo();
                    cigarChar = '?';
                    refPos = samRecord.get0BasedPosition();
                    if(!qualExcludeClips && (cigarPtr != NULL))
                    {
                        // Offset the reference position by any soft clips
                        // by subtracting the queryIndex of this start position.
                        // refPos is now the start position of the clips.
                        refPos -= cigarPtr->getQueryIndex(0);
                    }

                    while(qual[index] != 0)
                    {
                        // Skip this quality if it is clipped and we are skipping clips.
                        if(cigarPtr != NULL)