예제 #1
0
int main(int argc, char* argv[]) {

	string plsFileName;
	int advance;

	if (argc <= 2) {
		cout << "usage: testAdvance file.pls.h5 advance " << endl;
		cout << "move 'advance' reads forward in a file." << endl;
		exit(1);
	}
	plsFileName = argv[1];
	advance = atoi(argv[2]);

	
	ReaderAgglomerate reader;
	reader.Initialize(plsFileName);
	
  SMRTSequence seq;
  int seqIndex = 0;
	int i;
	for (i = 0; i < 4; i++ ){
		seq.Free();
		reader.Advance(advance);
		reader.GetNext(seq);
	}
	seq.PrintSeq(cout);
}
예제 #2
0
void MakeVirtualRead(SMRTSequence & smrtRead,
                     const vector<SMRTSequence> & subreads)
{
    assert(subreads.size() > 0);
    DNALength hqStart = 0, hqEnd = 0;
    for(auto subread: subreads) {
        hqStart = min(DNALength(subread.SubreadStart()), hqStart);
        hqEnd   = max(DNALength(subread.SubreadEnd()),   hqEnd);
    }
    smrtRead.Free();
    smrtRead.Allocate(hqEnd);
    memset(smrtRead.seq, 'N', sizeof(char) * hqEnd);
    smrtRead.lowQualityPrefix = hqStart;
    smrtRead.lowQualitySuffix = smrtRead.length - hqEnd;
    smrtRead.highQualityRegionScore = subreads[0].highQualityRegionScore;
    smrtRead.HoleNumber(subreads[0].HoleNumber());
    stringstream ss;
    ss << SMRTTitle(subreads[0].GetTitle()).MovieName() << "/" << subreads[0].HoleNumber();
    smrtRead.CopyTitle(ss.str());
    for (auto subread: subreads) {
        memcpy(&smrtRead.seq[subread.SubreadStart()],
               &subread.seq[0], sizeof(char) * subread.length);
    }
}
int main(int argc, char* argv[])
{
    std::string outFileName;
    unsigned contextLength = 5;
    int minSamples = 500;
    int maxSamples = 1000;
    if (argc < 3) {
        PrintUsage();
        std::exit(EXIT_FAILURE);
    }

    int argi = 1;
    std::string cmpH5FileName;
    cmpH5FileName = argv[argi++];
    outFileName = argv[argi++];
    int minAverageQual = 0;
    bool onlyMaxLength = false;

    while (argi < argc) {
        if (strcmp(argv[argi], "-contextLength") == 0) {
            contextLength = atoi(argv[++argi]);
        } else if (strcmp(argv[argi], "-minSamples") == 0) {
            minSamples = atoi(argv[++argi]);
        } else if (strcmp(argv[argi], "-maxSamples") == 0) {
            maxSamples = atoi(argv[++argi]);
        } else if (strcmp(argv[argi], "-onlyMaxLength") == 0) {
            onlyMaxLength = true;
        } else {
            PrintUsage();
            std::cout << "ERROR, bad option: " << argv[argi] << std::endl;
            std::exit(EXIT_FAILURE);
        }
        ++argi;
    }
    std::map<std::string, ScoredLength> maxLengthMap;
    OutputSampleListSet samples(contextLength);
    SMRTSequence read;

    std::ofstream sampleOut;
    CrucialOpen(outFileName, sampleOut, std::ios::out | std::ios::binary);
    int fileNameIndex;

    int numContextsReached = 0;
    int numContexts = 1 << (contextLength * 2);
    ReaderAgglomerate reader;
    samples.keyLength = contextLength;
    HDFCmpFile<CmpAlignment> cmpReader;
    cmpReader.IncludeField("QualityValue");
    cmpReader.IncludeField("DeletionQV");
    cmpReader.IncludeField("InsertionQV");
    cmpReader.IncludeField("SubstitutionQV");
    cmpReader.IncludeField("SubstitutionTag");
    cmpReader.IncludeField("DeletionTag");
    cmpReader.IncludeField("PulseIndex");
    cmpReader.IncludeField("WidthInFrames");
    cmpReader.IncludeField("PreBaseFrames");

    if (cmpReader.Initialize(cmpH5FileName, H5F_ACC_RDWR) == 0) {
        std::cout << "ERROR, could not open the cmp file." << std::endl;
        std::exit(EXIT_FAILURE);
    }
    std::cout << "Reading cmp file." << std::endl;

    CmpFile cmpFile;

    cmpReader.ReadAlignmentDescriptions(cmpFile);
    cmpReader.ReadStructure(cmpFile);
    std::cout << "done reading structure." << std::endl;
    int alignmentIndex;
    int nAlignments = cmpReader.alnInfoGroup.GetNAlignments();
    std::vector<int> alignmentToBaseMap;

    for (alignmentIndex = 0; alignmentIndex < nAlignments and !samples.Sufficient();
         alignmentIndex++) {
        //
        // For ease of use, store the length of the alignment to make another model.
        //

        ByteAlignment alignmentArray;
        cmpReader.ReadAlignmentArray(alignmentIndex, alignmentArray);
        Alignment alignment;
        ByteAlignmentToAlignment(alignmentArray, alignment);
        std::string readSequence, refSequence;
        readSequence.resize(alignmentArray.size());
        refSequence.resize(alignmentArray.size());
        DNASequence readDNA, refDNA;

        ByteAlignmentToQueryString(&alignmentArray[0], alignmentArray.size(), &readSequence[0]);
        ByteAlignmentToRefString(&alignmentArray[0], alignmentArray.size(), &refSequence[0]);
        RemoveGaps(readSequence, readSequence);
        RemoveGaps(refSequence, refSequence);

        readDNA.seq = (Nucleotide*)readSequence.c_str();
        readDNA.length = readSequence.size();
        refDNA.seq = (Nucleotide*)refSequence.c_str();
        refDNA.length = refSequence.size();
        CmpAlignment cmpAlignment;

        cmpReader.ImportReadFromCmpH5(alignmentIndex, cmpAlignment, read);

        CreateAlignmentToSequenceMap(alignmentArray, alignmentToBaseMap);

        if (read.length < contextLength) {
            continue;
        }
        int subreadLength = (cmpFile.alnInfo.alignments[alignmentIndex].GetQueryEnd() -
                             cmpFile.alnInfo.alignments[alignmentIndex].GetQueryStart());
        if (onlyMaxLength == false) {
            samples.lengths.push_back(subreadLength);
        } else {
            int score = (cmpAlignment.GetNMatch() - cmpAlignment.GetNMismatch() -
                         cmpAlignment.GetNInsertions() - cmpAlignment.GetNDeletions());
            std::stringstream nameStrm;
            nameStrm << cmpAlignment.GetMovieId() << "_" << cmpAlignment.GetHoleNumber();
            std::string nameStr = nameStrm.str();
            if (maxLengthMap.find(nameStr) == maxLengthMap.end()) {
                maxLengthMap[nameStr] = ScoredLength(score, subreadLength);
            }
        }

        int sampleEnd = alignmentArray.size() - contextLength / 2;
        int a;
        for (a = contextLength / 2; a < sampleEnd; a++) {

            // Make sure the context begins on a real nucleotide.
            while (a < sampleEnd and ((RefChar[alignmentArray[a]] == ' '))) {
                a++;
            }

            //
            // Move ab back to an index where there are contextLength/2 non-gap
            // characters, counted by nb
            //
            int ab;  //num bases
            int ae;  //alignment end
            ab = a - 1;
            int nb = 0, ne = 0;
            while (true) {
                if (RefChar[alignmentArray[ab]] != ' ') {
                    nb++;
                }
                if (ab == 0 or nb == static_cast<int>(contextLength) / 2) break;
                ab--;
            }

            //
            // Advance ae to an index where there are contextLength/2 non-gap
            // characters, counted by ne.
            //
            ae = a + 1;
            while (ae < static_cast<int>(alignmentArray.size()) and
                   ne < static_cast<int>(contextLength) / 2) {
                if (RefChar[alignmentArray[ae]] != ' ') {
                    ne++;
                }
                ae++;
            }

            //
            // Make sure there are no edge effects that prevent a context of the correct length from being assigned.
            //
            if (nb + ne + 1 != static_cast<int>(contextLength)) {
                continue;
            }
            int ai;
            std::string context;
            for (ai = ab; ai < ae; ai++) {
                if (RefChar[alignmentArray[ai]] != ' ') {
                    context.push_back(RefChar[alignmentArray[ai]]);
                }
            }
            assert(context.size() == contextLength);
            //
            // Now create the context.
            //
            OutputSample sample;

            //
            // This context is a deletion, create that.
            //
            sample.type = OutputSample::Deletion;

            //
            // This context is either an insertion or substitution
            //
            // Look to see if the previous aligned position was an
            // insertion, and move back as far as the insertion extends.
            int aq = a - 1;
            int sampleLength;

            if (QueryChar[alignmentArray[a]] == ' ') {
                sample.type = OutputSample::Deletion;
                sampleLength = 0;
            } else if (RefChar[alignmentArray[aq]] == ' ') {

                while (aq > 0 and RefChar[alignmentArray[aq]] == ' ' and
                       QueryChar[alignmentArray[aq]] != ' ') {
                    aq--;
                }
                sample.type = OutputSample::Insertion;
                sampleLength = a - aq;
            } else if (QueryChar[alignmentArray[a]] == RefChar[alignmentArray[aq]]) {
                sample.type = OutputSample::Match;
                sampleLength = 1;
            } else {
                sample.type = OutputSample::Substitution;
                sampleLength = 1;
            }

            sample.Resize(sampleLength);
            if (sampleLength > 0) {
                int seqPos = alignmentToBaseMap[aq];
                if (seqPos < static_cast<int>(read.length)) {
                    sample.CopyFromSeq(read, seqPos, sampleLength);
                    std::string nucs;
                    for (size_t n = 0; n < sample.nucleotides.size(); n++) {
                        char c = sample.nucleotides[n];
                        assert(c == 'A' or c == 'T' or c == 'G' or c == 'C');
                        nucs.push_back(sample.nucleotides[n]);
                    }
                }
            }
            samples.AppendOutputSample(context, sample);
        }
        read.Free();
    }

    if (onlyMaxLength) {
        std::map<std::string, ScoredLength>::iterator maxScoreIt;
        for (maxScoreIt = maxLengthMap.begin(); maxScoreIt != maxLengthMap.end(); ++maxScoreIt) {
            std::cout << maxScoreIt->second.length << std::endl;
            samples.lengths.push_back(maxScoreIt->second.length);
        }
    }

    samples.Write(sampleOut);

    return 0;
}
예제 #4
0
int main(int argc, char* argv[]) {
    string program = "pls2fasta";
    string versionString = VERSION;
    AppendPerforceChangelist(PERFORCE_VERSION_STRING, versionString);

	string plsFileName, fastaOutName;
	vector<string> plsFileNames;
	bool trimByRegion, maskByRegion;
	trimByRegion = false;
	maskByRegion = false;
	int argi = 3;
	RegionTable regionTable;
	string regionsFOFNName = "";
	vector<string> regionFileNames;
	bool splitSubreads = true;
	int minSubreadLength = 0;
	bool addSimulatedData = false;
	bool printSimulatedCoordinate = false;
	bool printSimulatedSequenceIndex = false;
  bool printFastq = false;
  bool printCcs   = false;
  int  lineLength = 50;
  int minReadScore = 0;
  vector<int> holeNumbers;
  CommandLineParser clp;
  bool printOnlyBest = false;

  clp.SetProgramName(program);
  clp.SetVersion(versionString);
  clp.RegisterStringOption("in.pls.h5", &plsFileName, "Input pls.h5/bax.h5/fofn file.", true);
  clp.RegisterStringOption("out.fasta", &fastaOutName, "Output fasta/fastq file.", true);
  clp.RegisterPreviousFlagsAsHidden();
  clp.RegisterFlagOption("trimByRegion", &trimByRegion, "Trim away low quality regions.");
  clp.RegisterFlagOption("maskByRegion", &maskByRegion, "Mask low quality regions with 'N'.");
  clp.RegisterStringOption("regionTable", &regionsFOFNName, "Optional HDF file with a /PulseData/Regions dataset.");
  clp.RegisterIntOption("minSubreadLength", &minSubreadLength, "Do not write subreads less than the specified length.", CommandLineParser::PositiveInteger);
  clp.RegisterFlagOption("noSplitSubreads", &splitSubreads, "Do not split reads on adapter sequences.");
  clp.RegisterIntListOption("holeNumber", &holeNumbers, "Only print this hole number (or list of numbers).");
  clp.RegisterFlagOption("fastq", &printFastq, "Print in FASTQ format with quality.");
  clp.RegisterFlagOption("ccs", &printCcs, "Print de novo CCS sequences");
  clp.RegisterIntOption("lineLength", &lineLength, "Specify fasta/fastq line length", CommandLineParser::PositiveInteger);
  clp.RegisterIntOption("minReadScore", &minReadScore, "Minimum read score to print a read.  The score is "
                        "a number between 0 and 1000 and represents the expected accuracy percentage * 10. "
                        "A typical value would be between 750 and 800.  This does not apply to ccs reads.", CommandLineParser::NonNegativeInteger);
  clp.RegisterFlagOption("best", &printOnlyBest, "If a CCS sequence exists, print this.  Otherwise, print the longest"
                         "subread.  This does not support fastq.");
  string description = ("Converts pls.h5/bax.h5/fofn files to fasta or fastq files. Although fasta files are provided"
  " with every run, they are not trimmed nor split into subreads. This program takes "
  "additional annotation information, such as the subread coordinates and high quality regions "
  "and uses them to create fasta sequences that are substrings of all bases called. Most of the time "
  "you will want to trim low quality reads, so you should specify -trimByRegion.");
  clp.SetProgramSummary(description);
                        
  clp.ParseCommandLine(argc, argv);

    cerr << "[INFO] " << GetTimestamp() << " [" << program << "] started."  << endl;
	if (trimByRegion and maskByRegion) {
		cout << "ERROR! You cannot both trim and mask regions. Use one or the other." << endl;
		exit(1);
	}
		 
  if (printFastq) {
    // Setting lineLength to 0 flags to print on one line.
    lineLength = 0;
  }

	if (FileOfFileNames::IsFOFN(plsFileName)) {
		FileOfFileNames::FOFNToList(plsFileName, plsFileNames);
	}
	else {
		plsFileNames.push_back(plsFileName);
	}
	if (regionsFOFNName == "") {
		regionFileNames = plsFileNames;
	}
	else {
		if (FileOfFileNames::IsFOFN(regionsFOFNName)) {
			FileOfFileNames::FOFNToList(regionsFOFNName, regionFileNames);
		}
		else {
			regionFileNames.push_back(regionsFOFNName);
		}
	}



	ofstream fastaOut;
	CrucialOpen(fastaOutName, fastaOut);
	int plsFileIndex;
	HDFRegionTableReader hdfRegionReader;
  sort(holeNumbers.begin(), holeNumbers.end());
	for (plsFileIndex = 0; plsFileIndex < plsFileNames.size(); plsFileIndex++) {
		if (trimByRegion or maskByRegion or splitSubreads) {
			hdfRegionReader.Initialize(regionFileNames[plsFileIndex]);
			hdfRegionReader.ReadTable(regionTable);
			regionTable.SortTableByHoleNumber();
		}
		
		ReaderAgglomerate reader;
    HDFBasReader ccsReader;

    if (printOnlyBest) {
      ccsReader.SetReadBasesFromCCS();
      ccsReader.Initialize(plsFileNames[plsFileIndex]);
    }
    if (printCcs == false) {
  		reader.IgnoreCCS();
    }
    else {
      reader.hdfBasReader.SetReadBasesFromCCS();
    }
		if (addSimulatedData) {
			reader.hdfBasReader.IncludeField("SimulatedCoordinate");
			reader.hdfBasReader.IncludeField("SimulatedSequenceIndex");
		}

        if (reader.SetReadFileName(plsFileNames[plsFileIndex]) == 0) {
          cout << "ERROR, could not determine file type."
               << plsFileNames[plsFileIndex] << endl;
          exit(1);
        }
        if (reader.Initialize() == 0) {
          cout << "ERROR, could not initialize file "
               << plsFileNames[plsFileIndex] << endl;
          exit(1);
        }

		DNALength simulatedCoordinate;
		DNALength simulatedSequenceIndex;
		reader.SkipReadQuality();
		SMRTSequence seq;
		vector<ReadInterval> subreadIntervals;;
    SMRTSequence ccsSeq;
		while (reader.GetNext(seq)) {
      if (printOnlyBest) {
        ccsReader.GetNext(ccsSeq);
      }

      if (holeNumbers.size() != 0 and 
          binary_search(holeNumbers.begin(), holeNumbers.end(), seq.zmwData.holeNumber) == false) {
        continue;
      }

      if (seq.length == 0) {
        continue;
      }

			if (addSimulatedData) {
				reader.hdfBasReader.simulatedCoordinateArray.Read(reader.hdfBasReader.curRead-1, reader.hdfBasReader.curRead, &simulatedCoordinate);
				reader.hdfBasReader.simulatedSequenceIndexArray.Read(reader.hdfBasReader.curRead-1, reader.hdfBasReader.curRead, &simulatedSequenceIndex);
			}

		  if (printCcs == true) {
        if (printFastq == false) {
          seq.PrintSeq(fastaOut);
        }
        else {
          seq.PrintFastq(fastaOut, lineLength);
        }
        continue;
      }	

      //
      // Determine the high quality boundaries of the read.  This is
      // the full read is no hq regions exist, or it is stated to
      // ignore regions.
      //
      DNALength hqReadStart, hqReadEnd;
      int hqRegionScore;
      if (GetReadTrimCoordinates(seq, seq.zmwData, regionTable, hqReadStart, hqReadEnd, hqRegionScore) == false or 
          (trimByRegion == false and maskByRegion == false)) {
        hqReadStart = 0;
        hqReadEnd   = seq.length;
      }
      
      //
      // Mask off the low quality portions of the reads.
      //
			if (maskByRegion) {
        if (hqReadStart > 0) {
          fill(&seq.seq[0], &seq.seq[hqReadStart], 'N');
        }
        if (hqReadEnd != seq.length) {
          fill(&seq.seq[hqReadEnd], &seq.seq[seq.length], 'N');
        }
			}
      


      //
      // Now possibly print the full read with masking.  This could be handled by making a 
      // 
			if (splitSubreads == false) {
        ReadInterval wholeRead(0, seq.length);
        // The set of subread intervals is just the entire read.
        subreadIntervals.clear();
        subreadIntervals.push_back(wholeRead);
			}
			else {
				//
				// Print subread coordinates no matter whether or not reads have subreads.
				//
				subreadIntervals.clear(); // clear old, new intervals are appended.
				CollectSubreadIntervals(seq, &regionTable, subreadIntervals);
      }
      //
      // Output all subreads as separate sequences.
      //
      int intvIndex;
      SMRTSequence bestSubreadSequence;
      int bestSubreadScore = -1;
      int bestSubreadIndex = 0;
      int bestSubreadStart = 0, bestSubreadEnd = 0;
      SMRTSequence bestSubread;
      for (intvIndex = 0; intvIndex < subreadIntervals.size(); intvIndex++) {
        SMRTSequence subreadSequence, subreadSequenceRC;
					
        subreadSequence.subreadStart = subreadIntervals[intvIndex].start;
        subreadSequence.subreadEnd   = subreadIntervals[intvIndex].end;
          
        // 
        // When trimming by region, only output the parts of the
        // subread that overlap the hq region.
        //
        if (trimByRegion == true) {
          subreadSequence.subreadStart = max((DNALength) subreadIntervals[intvIndex].start, hqReadStart);
          subreadSequence.subreadEnd   = min((DNALength) subreadIntervals[intvIndex].end, hqReadEnd);
        }

        if (subreadSequence.subreadStart >= subreadSequence.subreadEnd or 
            subreadSequence.subreadEnd - subreadSequence.subreadStart <= minSubreadLength) {
          //
          // There is no high qualty portion of this subread. Skip it.
          //
          continue;
        }

        if (hqRegionScore < minReadScore) {
          continue;
        }

        //
        // Print the subread, adding the coordinates as part of the title.
        //
        subreadSequence.ReferenceSubstring(seq, subreadSequence.subreadStart, 
                                           subreadSequence.subreadEnd - subreadSequence.subreadStart);
        stringstream titleStream;
        titleStream << seq.title;
        if (splitSubreads) {
          //
          // Add the subread coordinates if splitting on subread.
          //
          titleStream << "/" 
                      << subreadSequence.subreadStart
                      << "_" << subreadSequence.subreadEnd;
        }
          
        // 
        // If running on simulated data, add where the values were simulated from.
        //
        if (addSimulatedData) {
          titleStream << ((FASTASequence*)&seq)->title << "/chrIndex_" 
                      << simulatedSequenceIndex << "/position_"<< simulatedCoordinate;
          ((FASTASequence*)&seq)->CopyTitle(titleStream.str());
        }

        subreadSequence.CopyTitle(titleStream.str());

        //
        // Eventually replace with WriterAgglomerate.
        //
        if (printOnlyBest == false) {
          if (subreadSequence.length > 0) {
            if (printFastq == false) {
              ((FASTASequence*)&subreadSequence)->PrintSeq(fastaOut);
            }
            else {
              subreadSequence.PrintFastq(fastaOut, lineLength);
            }
          }
          delete[] subreadSequence.title;
        }
        else {
          int subreadWeightedScore = subreadSequence.length * hqRegionScore;
          if (subreadWeightedScore > bestSubreadScore) {
            bestSubreadIndex = intvIndex;
            bestSubread = subreadSequence;
            bestSubreadScore = subreadWeightedScore;
          }
        }
      }

      if (printOnlyBest) {
        if (ccsSeq.length > 0) {
          if (printFastq == false) {
            ccsSeq.PrintSeq(fastaOut);
          }
          else {
            ccsSeq.PrintFastq(fastaOut, ccsSeq.length);
          }
        }
        else {
          if (bestSubreadScore >= 0) {
            if (printFastq == false) {
              bestSubread.PrintSeq(fastaOut);
            }
            else {
              bestSubread.PrintFastq(fastaOut, bestSubread.length);
            }
            bestSubread.Free();
          }
        }
        ccsSeq.Free();
      }
      seq.Free();
    }
    reader.Close();
    hdfRegionReader.Close();
  }
  cerr << "[INFO] " << GetTimestamp() << " [" << program << "] ended."  << endl;
}
예제 #5
0
bool SubreadConverter::ConvertFile(HDFBasReader* reader,
                                   PacBio::BAM::BamWriter* writer,
                                   PacBio::BAM::BamWriter* scrapsWriter) 
{
    assert(reader);

    // initialize with default values (shared across all unmapped subreads)
    BamRecordImpl bamRecord;

    // read region table info
    std::unique_ptr<HDFRegionTableReader> const regionTableReader(new HDFRegionTableReader);
    RegionTable regionTable;
    string fn = filenameForReader_[reader];
    assert(!fn.empty());
    if (regionTableReader->Initialize(fn) == 0) {
        AddErrorMessage("could not read region table on "+fn);
        return false;
    }
    regionTable.Reset();
    regionTableReader->ReadTable(regionTable);
    regionTableReader->Close();

    // initialize read scores
    InitReadScores(reader);

    // fetch records from HDF5 file
    SMRTSequence smrtRecord;
    while (reader->GetNext(smrtRecord)) {

        // compute subread & adapter intervals
        SubreadInterval hqInterval;
        deque<SubreadInterval> subreadIntervals;
        deque<SubreadInterval> adapterIntervals;
        try {
            hqInterval = ComputeSubreadIntervals(&subreadIntervals,
                                                 &adapterIntervals,
                                                 regionTable,
                                                 smrtRecord.zmwData.holeNumber,
                                                 smrtRecord.length);
        } catch (runtime_error& e) {
            AddErrorMessage(string(e.what()));
            smrtRecord.Free();
            return false;
        }

        // sequencing ZMW
        if (IsSequencingZmw(smrtRecord))
        {
            // write subreads to main BAM file
            for (const SubreadInterval& interval : subreadIntervals)
            {
                // skip invalid or 0-sized intervals
                if (interval.End <= interval.Start)
                    continue;

                if (!WriteSubreadRecord(smrtRecord,
                                        interval.Start,
                                        interval.End,
                                        ReadGroupId(),
                                        static_cast<uint8_t>(interval.LocalContextFlags),
                                        writer))
                {
                    smrtRecord.Free();
                    return false;
                }
            }

            // if scraps BAM file present
            if (scrapsWriter)
            {
                // write 5-end LQ sequence
                if (hqInterval.Start > 0)
                {
                    if (!WriteLowQualityRecord(smrtRecord,
                                               0,
                                               hqInterval.Start,
                                               ScrapsReadGroupId(),
                                               scrapsWriter))
                    {
                        smrtRecord.Free();
                        return false;
                    }
                }

                // write adapters
                for (const SubreadInterval& interval : adapterIntervals) {

                    // skip invalid or 0-sized adapters
                    if (interval.End <= interval.Start)
                        continue;

                    if (!WriteAdapterRecord(smrtRecord,
                                            interval.Start,
                                            interval.End,
                                            ScrapsReadGroupId(),
                                            scrapsWriter))
                    {
                        smrtRecord.Free();
                        return false;
                    }
                }

                // write 3'-end LQ sequence
                if (hqInterval.End < smrtRecord.length)
                {
                    if (!WriteLowQualityRecord(smrtRecord,
                                               hqInterval.End,
                                               smrtRecord.length,
                                               ScrapsReadGroupId(),
                                               scrapsWriter))
                    {
                        smrtRecord.Free();
                        return false;
                    }
                }
            }
        } // sequencing ZMW

        // non-sequencing ZMW
        else
        {
            assert(!IsSequencingZmw(smrtRecord));

            // only write these if scraps BAM present & we are in 'internal mode'
            if (settings_.isInternal && scrapsWriter)
            {
                // write 5-end LQ sequence to scraps BAM
                if (hqInterval.Start > 0)
                {
                    if (!WriteLowQualityRecord(smrtRecord,
                                               0,
                                               hqInterval.Start,
                                               ScrapsReadGroupId(),
                                               scrapsWriter))
                    {
                        smrtRecord.Free();
                        return false;
                    }
                }

                // write subreads & adapters to scraps BAM, sorted by query start
                while (!subreadIntervals.empty() && !adapterIntervals.empty()) {

                    const SubreadInterval& subread = subreadIntervals.front();
                    const SubreadInterval& adapter = adapterIntervals.front();
                    assert(subread.Start != adapter.Start);

                    if (subread.Start < adapter.Start)
                    {
                        if (!WriteFilteredRecord(smrtRecord,
                                                 subread.Start,
                                                 subread.End,
                                                 ScrapsReadGroupId(),
                                                 static_cast<uint8_t>(subread.LocalContextFlags),
                                                 scrapsWriter))
                        {
                            smrtRecord.Free();
                            return false;
                        }

                        subreadIntervals.pop_front();
                    }
                    else
                    {
                        if (!WriteAdapterRecord(smrtRecord,
                                                adapter.Start,
                                                adapter.End,
                                                ScrapsReadGroupId(),
                                                scrapsWriter))
                        {
                            smrtRecord.Free();
                            return false;
                        }
                        adapterIntervals.pop_front();
                    }
                }

                // flush any traling subread intervals
                while (!subreadIntervals.empty())
                {
                    assert(adapterIntervals.empty());
                    const SubreadInterval& subread = subreadIntervals.front();
                    if (!WriteFilteredRecord(smrtRecord,
                                             subread.Start,
                                             subread.End,
                                             ScrapsReadGroupId(),
                                             static_cast<uint8_t>(subread.LocalContextFlags),
                                             scrapsWriter))
                    {
                        smrtRecord.Free();
                        return false;
                    }

                    subreadIntervals.pop_front();
                }

                // flush any remaining adapter intervals
                while (!adapterIntervals.empty())
                {
                    assert(subreadIntervals.empty());
                    const SubreadInterval& adapter = adapterIntervals.front();
                    if (!WriteAdapterRecord(smrtRecord,
                                            adapter.Start,
                                            adapter.End,
                                            ScrapsReadGroupId(),
                                            scrapsWriter))
                    {
                        smrtRecord.Free();
                        return false;
                    }
                    adapterIntervals.pop_front();
                }

                // write 3'-end LQ sequence to scraps BAM
                if (hqInterval.End < smrtRecord.length)
                {
                    if (!WriteLowQualityRecord(smrtRecord,
                                               hqInterval.End,
                                               smrtRecord.length,
                                               ScrapsReadGroupId(),
                                               scrapsWriter))
                    {
                        smrtRecord.Free();
                        return false;
                    }
                }
            }
        } // non-sequencing ZMW

        smrtRecord.Free();
    }

    // if we get here, all OK
    return true; 
} 
예제 #6
0
int main(int argc, char* argv[]) {
	
	string genomeFileName, readsFileName;
	TupleMetrics tm;
	float insRate = 0.10;
	tm.tupleSize = 8;
	CommandLineParser clp;
	int nProcessors = 1;
	clp.SetProgramName("exhalign");
	clp.SetProgramSummary("Count the number of occurrences of every k-mer in a file.");
	clp.RegisterStringOption("genome", &genomeFileName, "The file of the genome to align to.");
	clp.RegisterStringOption("reads",  &readsFileName,  "The reads to align.");
	clp.RegisterPreviousFlagsAsHidden();
	clp.RegisterIntOption("wordsize", &tm.tupleSize, "Size of words to count", 
												CommandLineParser::NonNegativeInteger);
	clp.RegisterFloatOption("insrate", &insRate, "Roughly the insertion rate (10%)", 
													CommandLineParser::NonNegativeFloat);
	clp.RegisterIntOption("nProc", &nProcessors, "Number of processors to use", CommandLineParser::NonNegativeInteger);
	clp.ParseCommandLine(argc, argv);

	insRate+=1.0;
	//
	// Process the reads into a vector of read keywords
	//
	

	vector<string> readsFileNames;
	vector<FASTQSequence> reads;
	vector<vector<ReadKeyword> > keywords;
	SMRTSequence seq, seqRC;
	ReadKeyword keyword;
	int readIndex = 0;

	if (FileOfFileNames::IsFOFN(readsFileName)) {
		FileOfFileNames::FOFNToList(readsFileName, readsFileNames);
	}
	else {
		readsFileNames.push_back(readsFileName);
	}

	ReaderAgglomerate genomeReader;	
	HDFRegionTableReader regionTableReader;
	genomeReader.Initialize(genomeFileName);
	FASTQSequence genome;
	genomeReader.GetNext(genome);
	SubreadIterator subreadIterator;

	keywords.resize(nProcessors);
	RegionTable  regionTable, *regionTablePtr;

	int readsFileIndex;
	for (readsFileIndex = 0; readsFileIndex < readsFileNames.size(); readsFileIndex++ ) {
		
		ReaderAgglomerate reader;
		reader.Initialize(readsFileNames[readsFileIndex]);
		regionTalePtr = NULL;
		
		if (reader.fileType == HDFPulse or
				reader.fileType == HDFBase) {
			regionTableReader.Initialize(readsFileNames[readsFileIndex]);
			regionTableReader.Read(regionTable);
			regionTablePtr = &regionTable;
		}
		else {
			regionTablePtr = NULL;
		}
		SMRTSequence fullSequence;
		while(reader.GetNext(fullSequence)) {

			subreadIterator.Initialize(&fullSequence, regionTablePtr);
			
			SMRTSequence seq;
			while (subreadIterator.GetNext(seq)) {
				DNALength pos;
				if (seq.length < tm.tupleSize) 
					continue;
				reads.push_back(seq);
				for (pos = 0; pos < seq.length - tm.tupleSize + 1; pos++) {
					keyword.tuple.FromStringLR(&seq.seq[pos], tm);
					keyword.readPos = pos;
					keyword.readIndex = readIndex;
					keywords[(readIndex/2)%nProcessors].push_back(keyword);
				}
				readIndex++;
				seq.MakeRC(seqRC);
				reads.push_back(seqRC);
				for (pos = 0; pos < seqRC.length - tm.tupleSize + 1; pos++) {
					keyword.tuple.FromStringLR(&seqRC.seq[pos], tm);
					keyword.readPos = pos;
					keyword.readIndex = readIndex;
					keywords[(readIndex/2)%nProcessors].push_back(keyword);
				}
				readIndex++;
				//				seq.Free();
				seqRC.Free();
			}
			fullSequence.Free();
		}
	}
	int procIndex;
	for (procIndex = 0; procIndex < nProcessors; procIndex++) {
		std::sort(keywords[procIndex].begin(), keywords[procIndex].end());
	}


  std::vector<int> prevAlignedGenomePos;
  std::vector<int> readOptScore;
  std::vector<FastqAlignment > optAlignment;
	std::vector<int> optGenomeAlignPos;
	std::vector<int> optGenomeAlignLength;

  prevAlignedGenomePos.resize(reads.size());
  readOptScore.resize(reads.size());
  optAlignment.resize(reads.size());
	optGenomeAlignPos.resize(reads.size());
	optGenomeAlignLength.resize(reads.size());
	vector<Data> tdata;
	tdata.resize(nProcessors);
  std::fill(prevAlignedGenomePos.begin(), prevAlignedGenomePos.end(), -1);
	for (procIndex = 0; procIndex < nProcessors; procIndex++) {
		tdata[procIndex].prevAlignedGenomePos = &prevAlignedGenomePos;
		tdata[procIndex].readOptScore         = &readOptScore;
		tdata[procIndex].optAlignment         = &optAlignment;
		tdata[procIndex].optGenomeAlignPos    = &optGenomeAlignPos;
		tdata[procIndex].optGenomeAlignLength = &optGenomeAlignLength;
		tdata[procIndex].keywords             = &keywords[procIndex];
		tdata[procIndex].genome               = &genome;
		tdata[procIndex].insRate              = insRate;
		tdata[procIndex].reads                = &reads;
		tdata[procIndex].tm                   = &tm;
	}
	if (nProcessors == 1) {
		KeywordSeededAlignment(&tdata[0]);
	}
	else {
		pthread_t *threads = new pthread_t[nProcessors];
		pthread_attr_t *threadAttr = new pthread_attr_t[nProcessors];
		for (procIndex = 0; procIndex < nProcessors; procIndex++) {
			pthread_attr_init(&threadAttr[procIndex]);			
			pthread_create(&threads[procIndex], &threadAttr[procIndex], (void*(*)(void*))KeywordSeededAlignment, &tdata[procIndex]);
		}
		for (procIndex = 0; procIndex < nProcessors; procIndex++) {
			pthread_join(threads[procIndex], NULL);
		}

	}
	VectorIndex i;
	//	cout << "printing alignments for " << reads.size() << " reads." << endl;
	for (readIndex = 0; readIndex < readOptScore.size(); readIndex +=2 ){
		int optIndex = readIndex;
		if (readOptScore[readIndex] > readOptScore[readIndex+1]) {
			optIndex= readIndex + 1;
		}
		FASTQSequence genomeSubstring;
		genomeSubstring.seq = &genome.seq[optGenomeAlignPos[optIndex]];
		genomeSubstring.length =  optGenomeAlignLength[optIndex];
		if (prevAlignedGenomePos[optIndex] >= 0) {
			optAlignment[optIndex].qName.assign(reads[optIndex].title, reads[optIndex].titleLength);
			optAlignment[optIndex].tName.assign(genome.GetName());
			ComputeAlignmentStats(optAlignment[optIndex], reads[optIndex].seq, genomeSubstring.seq, SMRTDistanceMatrix, 6, 6);
			if (optAlignment[optIndex].blocks.size() > 0) {
				PrintCompareSequencesAlignment(optAlignment[optIndex], reads[optIndex], genomeSubstring,cout);
			}
			/*			StickPrintAlignment(optAlignment[optIndex],
													reads[optIndex],
													genomeSubstring, cout, 0, optGenomeAlignPos[optIndex]);
			*/
						
		}
	}
	for (readIndex = 0; readIndex < readOptScore.size(); readIndex++ ) {
		reads[readIndex].Free();
	}

	return 0;
}
예제 #7
0
bool HqRegionConverter::ConvertFile(HDFBasReader* reader,
                                    PacBio::BAM::BamWriter* writer,
                                    PacBio::BAM::BamWriter* scrapsWriter) 
{
    assert(reader);

    // read region table info
    std::unique_ptr<HDFRegionTableReader> const regionTableReader(new HDFRegionTableReader);
    RegionTable regionTable;
    std::string fn = filenameForReader_[reader];
    assert(!fn.empty());
    if (regionTableReader->Initialize(fn) == 0) {
        AddErrorMessage("could not read region table on "+fn);
        return false;
    }
    regionTable.Reset();
    regionTableReader->ReadTable(regionTable);
    regionTableReader->Close();

    // initialize read scores
    InitReadScores(reader);

    // fetch records from HDF5 file
    SMRTSequence smrtRecord;
    int hqStart, hqEnd, score;
    while (reader->GetNext(smrtRecord)) {

        // attempt get high quality region
        if (!LookupHQRegion(smrtRecord.zmwData.holeNumber,
                            regionTable,
                            hqStart,
                            hqEnd,
                            score))
        {
            stringstream s;
            s << "could not find HQ region for hole number: " << smrtRecord.zmwData.holeNumber;
            AddErrorMessage(s.str());
            smrtRecord.Free();
            return false;
        }

        // Catch and repair 1-off errors in the HQ region
        hqEnd = (hqEnd == static_cast<int>(smrtRecord.length)-1) ? smrtRecord.length
                                                                 : hqEnd;

        // sequencing ZMW
        if (IsSequencingZmw(smrtRecord))
        {
            // write HQRegion to main BAM file
            if (hqStart < hqEnd)
            {
                if (!WriteRecord(smrtRecord,
                                 hqStart,
                                 hqEnd,
                                 ReadGroupId(),
                                 writer))
                {
                    smrtRecord.Free();
                    return false;
                }
            }

            // if scraps BAM file present
            if (scrapsWriter)
            {
                // write 5'-end LQ sequence
                if (hqStart > 0)
                {
                    if (!WriteLowQualityRecord(smrtRecord,
                                               0,
                                               hqStart,
                                               ScrapsReadGroupId(),
                                               scrapsWriter))
                    {
                        smrtRecord.Free();
                        return false;
                    }
                }

                // write 3'-end LQ sequence
                if (static_cast<size_t>(hqEnd) < smrtRecord.length)
                {
                    if (!WriteLowQualityRecord(smrtRecord,
                                               hqEnd,
                                               smrtRecord.length,
                                               ScrapsReadGroupId(),
                                               scrapsWriter))
                    {
                        smrtRecord.Free();
                        return false;
                    }
                }
            }
        }

        // non-sequencing ZMW
        else
        {
            assert(!IsSequencingZmw(smrtRecord));

            // only write these if scraps BAM present & we are in 'internal mode'
            if (settings_.isInternal && scrapsWriter)
            {
                // write 5'-end LQ sequence
                if (hqStart > 0)
                {
                    if (!WriteLowQualityRecord(smrtRecord,
                                               0,
                                               hqStart,
                                               ScrapsReadGroupId(),
                                               scrapsWriter))
                    {
                        smrtRecord.Free();
                        return false;
                    }
                }

                // write HQRegion to scraps BAM file
                if (hqStart < hqEnd)
                {
                    if (!WriteFilteredRecord(smrtRecord,
                                             hqStart,
                                             hqEnd,
                                             ScrapsReadGroupId(),
                                             scrapsWriter))
                    {
                        smrtRecord.Free();
                        return false;
                    }
                }

                // write 3'-end LQ sequence
                if (static_cast<size_t>(hqEnd) < smrtRecord.length)
                {
                    if (!WriteLowQualityRecord(smrtRecord,
                                               hqEnd,
                                               smrtRecord.length,
                                               ScrapsReadGroupId(),
                                               scrapsWriter))
                    {
                        smrtRecord.Free();
                        return false;
                    }
                }
            }
        }

        smrtRecord.Free();
    }

    // if we get here, all OK
    return true;
}
예제 #8
0
int main(int argc, char* argv[]) {
    string refGenomeFileName = "";
    string lengthModelFileName = "";
    string outputModelFileName = "";
    DNALength numBasesPerFile = 0;
    string sourceReadsFileName = "";
    string titleTableFileName = "";
    int numBasH5Files = 1;
    string basH5BaseFileName = "simulated";
    string movieName = "m101211_092754_00114_cSIM_s1_p0";
    bool   doRandGenInit = true;
    bool   usePosMap     = false;
    bool   printPercentRepeat = false;
    string posMapFileName = "";
    vector<string> movieNames;
    bool useLengthModel = false;
    bool useFixedLength = false;
    ofstream posMapFile;
    int scaledLength = 0;
    int fixedLength = 0;
    int nBasFiles = 1;
    bool useLengthsModel = true;
    bool printHelp = false;


    //  Look to see if the refAsReads flag is specified anywhere before
    //  parsing the command line.

    CommandLineParser clp;
    string commandLine;
    string helpString;
    SetHelp(helpString);
    vector<string> fns;

    clp.RegisterStringOption("genome", &refGenomeFileName, "");
    clp.RegisterIntOption("numBasesPerFile", (int*)&numBasesPerFile, "",
                          CommandLineParser::PositiveInteger);
    clp.RegisterStringOption("sourceReads", &sourceReadsFileName, "");
    clp.RegisterStringOption("lengthModel", &lengthModelFileName, "");
    clp.RegisterIntOption("fixedLength", &fixedLength, "",
                          CommandLineParser::PositiveInteger);
    clp.RegisterFlagOption("lengthModel", &useLengthModel, "");
    clp.RegisterStringOption("movieName", &movieName, "");
    clp.RegisterStringOption("titleTable", &titleTableFileName, "");
    clp.RegisterStringOption("baseFileName", &basH5BaseFileName, "");
    clp.RegisterIntOption("nFiles", &nBasFiles, "",
                          CommandLineParser::PositiveInteger);
    clp.RegisterIntOption("meanLength", &scaledLength, "",
                          CommandLineParser::PositiveInteger);
    clp.RegisterStringOption("posMap", &posMapFileName, "");
    clp.RegisterFlagOption("printPercentRepeat", &printPercentRepeat, "");
    clp.RegisterFlagOption("h", &printHelp, "");

    clp.SetHelp(helpString);
    clp.ParseCommandLine(argc, argv, fns);
    clp.CommandLineToString(argc, argv, commandLine);

    clp.SetProgramName("alchemy");

    outputModelFileName = fns[0];
    if (argc <= 1 or printHelp or outputModelFileName == "") {
        cout << helpString << endl;
        exit(0);
    }

    if (usePosMap) {
        CrucialOpen(posMapFileName, posMapFile, std::ios::out);
    }

    if (sourceReadsFileName == "" and fixedLength == 0) {
        useLengthModel = true;
    }

    if (useLengthModel and fixedLength != 0) {
        cout << "ERROR! You must either use a length model or a fixed length." << endl;
        exit(1);
    }

    if (sourceReadsFileName == "" and numBasesPerFile == 0) {
        cout << "ERROR! You must specify either a set of read to use as " << endl
             << "original reads for simulation or the total number of bases " << endl
             << "to simulate in each bas.h5 file." << endl;
        exit(1);
    }

    if (sourceReadsFileName == "" and refGenomeFileName == "") {
        cout << "ERROR! You must specify a genome to sample reads from or a set of read "<<endl
             << "to use as original reads for simulation." << endl;
        exit(1);
    }

    if (fixedLength != 0 and refGenomeFileName == "") {
        cout << "ERROR! You must specify a genome file if using a fixed length." << endl;
        exit(1);
    }

    if ((fixedLength != 0 or scaledLength != 0) and sourceReadsFileName != "") {
        cout << "ERROR! You cannot specify a fixed length nor mean length with a source " << endl
             << "reads file.  The read lengths are taken from the source reads or the length model." << endl;
        exit(1);
    }

    LengthHistogram   lengthHistogram;
    OutputSampleListSet   outputModel(0);
    TitleTable titleTable;

    if (doRandGenInit) {
        InitializeRandomGeneratorWithTime();
    }

    //
    // Read models.
    //
    if (titleTableFileName != "") {
        titleTable.Read(titleTableFileName);
    }


    outputModel.Read(outputModelFileName);

    if (useLengthModel) {
        lengthHistogram.BuildFromAlignmentLengths(outputModel.lengths);
    }


    vector<int> alignmentLengths;
    int meanAlignmentLength;


    if (scaledLength != 0 and useLengthModel) {
        //
        // Scale the histogram so that the average length is 'scaledLength'.
        //

        // 1. Integrate histogram
        long totalLength = 0;
        long totalSamples = 0;
        int hi;
        for (hi = 0; hi < lengthHistogram.lengthHistogram.cdf.size()-1; hi++) {
            int ni;
            ni = lengthHistogram.lengthHistogram.cdf[hi+1] - lengthHistogram.lengthHistogram.cdf[hi];
            totalLength += ni * lengthHistogram.lengthHistogram.data[hi];
        }
        totalSamples = lengthHistogram.lengthHistogram.cdf[lengthHistogram.lengthHistogram.cdf.size()-1];

        float meanSampleLength = totalLength / (1.0*totalSamples);
        float fractionIncrease = scaledLength / meanSampleLength;

        for (hi = 0; hi < lengthHistogram.lengthHistogram.cdf.size(); hi++) {
            lengthHistogram.lengthHistogram.data[hi] *= fractionIncrease;
        }
    }

    FASTAReader inReader, seqReader;
    vector<FASTASequence> reference;
    DNALength refLength = 0;
    int i;
    if (refGenomeFileName != "") {
        inReader.Init(refGenomeFileName);
        inReader.ReadAllSequences(reference);

        for (i = 0; i < reference.size(); i++) {
            refLength += reference[i].length;
        }
    }

    if (sourceReadsFileName !=  "") {
        seqReader.Init(sourceReadsFileName);
    }

    ofstream readsFile;

    //
    // Create and simulate bas.h5 files.
    //
    int baseFileIndex;
    bool readsRemain = true;
    for (baseFileIndex = 0; ((sourceReadsFileName == "" and baseFileIndex < nBasFiles)  // case 1 is reads are generated by file
                             or (sourceReadsFileName != "" and readsRemain)); // case 2 is reads are generated by an input file.
            baseFileIndex++) {
        //
        // Prep the base file for writing.
        //
        stringstream fileNameStrm, movieNameStrm;
        //string movieName = "m000000_000000_00000_cSIMULATED_s";
        movieNameStrm << movieName << baseFileIndex << "_p0";
        string fullMovieName = movieNameStrm.str();
        fileNameStrm  << fullMovieName <<  ".bas.h5";


        HDFBasWriter basWriter;
        HDFRegionTableWriter regionWriter;
        //
        // This is mainly used to create the atributes.
        //
        RegionTable regionTable;
        regionTable.CreateDefaultAttributes();

        basWriter.SetPlatform(Springfield);
        //
        // Use a fixed set of fields for now.
        //

        // These are all pulled from the outputModel.
        basWriter.IncludeField("Basecall");
        basWriter.IncludeField("QualityValue");
        basWriter.IncludeField("SubstitutionQV");
        basWriter.IncludeField("SubstitutionTag");
        basWriter.IncludeField("InsertionQV");
        basWriter.IncludeField("DeletionQV");
        basWriter.IncludeField("DeletionTag");
        basWriter.IncludeField("WidthInFrames");
        basWriter.IncludeField("PreBaseFrames");
        basWriter.IncludeField("PulseIndex");

        vector<unsigned char> qualityValue, substitutionQV, substitutionTag, insertionQV, deletionQV, deletionTag;
        vector<HalfWord> widthInFrames, preBaseFrames, pulseIndex;

        // Just go from 0 .. hole Number
        basWriter.IncludeField("HoleNumber");
        // Fixed to 0.
        basWriter.IncludeField("HoleXY");
        if (usePosMap == false) {
            basWriter.IncludeField("SimulatedSequenceIndex");
            basWriter.IncludeField("SimulatedCoordinate");
        }
        basWriter.SetChangeListID("1.3.0.50.104380");


        DNALength numSimulatedBases  = 0;
        FASTASequence sampleSeq;
        //sampleSeq.length = readLength;
        int maxRetry = 10000000;
        int retryNumber = 0;
        int numReads = 0;
        int readLength = 0;

        while (numBasesPerFile == 0 or numSimulatedBases < numBasesPerFile) {
            DNALength seqIndex, seqPos;
            if (useLengthModel or fixedLength) {
                if (useLengthModel) {
                    lengthHistogram.GetRandomLength(readLength);
                }
                else {
                    readLength = fixedLength;
                }
            }
            if (refGenomeFileName != "") {
                FindRandomPos(reference, seqIndex, seqPos, readLength + (outputModel.keyLength - 1));
                sampleSeq.seq    = &reference[seqIndex].seq[seqPos];
                sampleSeq.length = readLength + (outputModel.keyLength - 1);
                assert(reference[seqIndex].length >= sampleSeq.length);
            }
            else if (sourceReadsFileName != "") {
                if (seqReader.GetNext(sampleSeq) == false) {
                    readsRemain = false;
                    break;
                }
                if (sampleSeq.length < outputModel.keyLength) {
                    continue;
                }
                //
                // Now attempt to parse the position from the fasta title.
                //

                if (useLengthModel) {
                    int tryNumber = 0;
                    readLength = 0;
                    int maxNTries = 1000;
                    int tryBuffer[5] = {-1,-1,-1,-1,-1};
                    while (tryNumber < maxNTries and readLength < outputModel.keyLength) {
                        lengthHistogram.GetRandomLength(readLength);
                        readLength = sampleSeq.length = min(sampleSeq.length, (unsigned int) readLength);
                        tryBuffer[tryNumber%5] = readLength;
                        tryNumber++;
                    }
                    if (tryNumber >= maxNTries) {
                        cout << "ERROR. Could not generate a read length greater than the " << outputModel.keyLength << " requried " <<endl
                             << "minimum number of bases using the length model specified in the alchemy." <<endl
                             << "model.  Something is either wrong with the model or the context length is too large." <<endl;
                        cout << "The last few tries were: " << tryBuffer[0] << " " << tryBuffer[1] << " " << tryBuffer[2] << " " << tryBuffer[3] << " " << tryBuffer[4] << endl;
                        exit(1);
                    }
                }

                readLength = sampleSeq.length;
                vector<string> tokens;
                Tokenize(sampleSeq.title, "|", tokens);
                if (tokens.size() == 4) {
                    seqPos = atoi(tokens[2].c_str());
                    if (titleTableFileName == "") {
                        seqIndex = 0;
                    }
                    else {
                        int index;
                        titleTable.Lookup(tokens[1], index);
                        seqIndex = index;
                    }
                }
                else {
                    seqPos   = 0;
                }
            }

            //
            // If this is the first read printed to the base file, initialize it.
            //
            if (numSimulatedBases == 0) {
                basWriter.Initialize(fileNameStrm.str(), movieNameStrm.str(), Springfield);
                regionWriter.Initialize(basWriter.pulseDataGroup);
            }

            numSimulatedBases += readLength;

            int p;
            // create the sample sequence
            int contextLength = outputModel.keyLength;
            int contextMiddle = contextLength / 2;
            string outputString;

            int nDel = 0;
            int nIns = 0;

            //
            // Simulate to beyond the sample length.
            //
            qualityValue.clear();
            substitutionQV.clear();
            substitutionTag.clear();
            insertionQV.clear();
            deletionQV.clear();
            deletionTag.clear();
            pulseIndex.clear();
            widthInFrames.clear();
            preBaseFrames.clear();
            assert(sampleSeq.length > contextMiddle + 1);
            for (p = contextMiddle;
                    p < sampleSeq.length - contextMiddle - 1; p++) {
                string refContext;
                refContext.assign((const char*) &sampleSeq.seq[p-contextMiddle], contextLength);

                string outputContext;
                int    contextWasFound;
                OutputSample sample;
                int i;
                for (i = 0; i < refContext.size(); i++) {
                    refContext[i] = toupper(refContext[i]);
                }
                outputModel.SampleRandomSample(refContext, sample);

                if (sample.type == OutputSample::Deletion ) {
                    //
                    // There was a deletion.  Advance in reference, then output
                    // the base after the deletion.
                    //
                    p++;
                    ++nDel;
                }

                int cp;
                //
                // Add the sampled context, possibly multiple characters because of an insertion.
                //
                for (i = 0; i < sample.nucleotides.size(); i++) {
                    outputString.push_back(sample.nucleotides[i]);
                    qualityValue.push_back(sample.qualities[i].qv[0]);
                    deletionQV.push_back(sample.qualities[i].qv[1]);
                    insertionQV.push_back(sample.qualities[i].qv[2]);
                    substitutionQV.push_back(sample.qualities[i].qv[3]);
                    deletionTag.push_back(sample.qualities[i].tags[0]);
                    substitutionTag.push_back(sample.qualities[i].tags[1]);
                    pulseIndex.push_back(sample.qualities[i].frameValues[0]);
                    preBaseFrames.push_back(sample.qualities[i].frameValues[1]);
                    widthInFrames.push_back(sample.qualities[i].frameValues[2]);
                }
                nIns += sample.qualities.size() - 1;
            }
            if (outputString.find('N') != outputString.npos or
                    outputString.find('n') != outputString.npos) {
                cout << "WARNING!  The sampled string " << endl << outputString << endl
                     << "should not contain N's, but it seems to.  This is being ignored "<<endl
                     << "for now so that simulation may continue, but this shouldn't happen"<<endl
                     << "and is really a bug." << endl;
                numSimulatedBases -= readLength;
                continue;
            }
            //
            // Ok, done creating the read, now time to create some quality values!!!!!
            //
            SMRTSequence read;
            read.length = outputString.size();
            read.Allocate(read.length);
            memcpy(read.seq, outputString.c_str(), read.length * sizeof(unsigned char));
            assert(qualityValue.size() == read.length * sizeof(unsigned char));
            memcpy(read.qual.data, &qualityValue[0], read.length * sizeof(unsigned char));
            memcpy(read.deletionQV.data, &deletionQV[0], read.length * sizeof(unsigned char));
            memcpy(read.insertionQV.data, &insertionQV[0], read.length * sizeof(unsigned char));
            memcpy(read.substitutionQV.data, &substitutionQV[0], read.length * sizeof(unsigned char));
            memcpy(read.deletionTag, &deletionTag[0], read.length * sizeof(unsigned char));
            memcpy(read.substitutionTag, &substitutionTag[0], read.length * sizeof(unsigned char));
            memcpy(read.pulseIndex, &pulseIndex[0], read.length * sizeof(int));
            memcpy(read.preBaseFrames, &preBaseFrames[0], read.length * sizeof(HalfWord));
            memcpy(read.widthInFrames, &widthInFrames[0], read.length * sizeof(HalfWord));

            //
            // The pulse index for now is just fake data.
            //
            int i;
            for (i = 0; i < read.length; i++) {
                read.pulseIndex[i] = 1;
            }
            read.xy[0] = seqIndex;
            read.xy[1] = seqPos;
            read.zmwData.holeNumber = numReads;

            basWriter.Write(read);
            // Record where this was simulated from.
            if (usePosMap == false) {
                basWriter.WriteSimulatedCoordinate(seqPos);
                basWriter.WriteSimulatedSequenceIndex(seqIndex);
            }
            else {
                posMapFile << fullMovieName << "/" << numReads << "/0_" << read.length << " " << seqIndex << " "<< seqPos;
                if (printPercentRepeat) {
                    DNALength nRepeat = sampleSeq.GetRepeatContent();
                    posMapFile << " " << nRepeat*1.0/sampleSeq.length;
                }
                posMapFile << endl;
            }
            RegionAnnotation region;
            region.row[0] = read.zmwData.holeNumber;
            region.row[1] = 1;
            region.row[2] = 0;
            region.row[3] = read.length;
            region.row[4] = 1000; // Should be enough.
            regionWriter.Write(region);
            region.row[1] = 2; // Rewrite for hq region encompassing everything.
            regionWriter.Write(region);
            if (sourceReadsFileName != "") {
                sampleSeq.Free();
            }
            read.Free();
            ++numReads;
        }
        regionWriter.Finalize(regionTable.columnNames,
                              regionTable.regionTypes,
                              regionTable.regionDescriptions,
                              regionTable.regionSources);
        basWriter.Close();
        numReads = 0;
        //
        // The bas writer should automatically flush on closing.
        //
    }
    if (usePosMap) {
        posMapFile.close();
    }

    for (i = 0; i < reference.size(); i++) {
        reference[i].Free();
    }
}
예제 #9
0
int main(int argc, char* argv[]) {

	string cmpFileName, movieFileName;

	int argi = 3;
	int numMetrics = 8;
	map<string,bool> metricOptions;
	int maxElements = 0;
	//
	// Default is all options are true
	//
	CreateMetricOptions(metricOptions);
	string metricList = "";
  bool useCcs = false;
  bool byRead = false;
  bool failOnMissingData = false;
  CommandLineParser clp;
  bool printVersion = false;

  clp.RegisterStringOption("basFileName", &movieFileName, "The input {bas,pls}.h5 or input.fofn.", true);
  clp.RegisterStringOption("cmpFileName", &cmpFileName, "The cmp.h5 file to load pulse information into.", true);
  clp.RegisterPreviousFlagsAsHidden();
  clp.RegisterStringOption("metrics", &metricList, "The a string delimited list of metrics (with no spaces).The "
                           "valid options are:  QualityValue, ClassifierQV, MergeQV, StartFrame,"
                           "PulseWidth, pkmid, IPD, and Light.");
  clp.RegisterFlagOption("useccs", &useCcs, "Load pulse information for CCS sequences and not raw bases.");
  clp.RegisterFlagOption("byread", &byRead, "Load pulse information by read rather than buffering an entire pls.h5 file.  "
                         "This option will soon be deprecated and on by default.");
  clp.RegisterIntOption("maxElements", &maxElements, "Set a limit on the size of pls/bas file to buffer in.", CommandLineParser::PositiveInteger);
  clp.RegisterFlagOption("failOnMissingData", &failOnMissingData, "Exit if any data fields are missing from the bas.h5 or pls.h5 input that are required to load a metric. Defualt is a warning.");

  clp.SetProgramSummary("Load pulse information such as inter pulse distance, or quality information into the cmp.h5 file."
                        "This allows one to analyze kinetic and quality information by alignment column.");
  clp.ParseCommandLine(argc, argv);

  if (printVersion) {
    cout << VERSION << endl;
    exit(1);
  }

	if (metricList == "") {
		SetDefaultMetricOptions(metricOptions);
	}
  else {
    ParseMetricsList(metricList, metricOptions);
  }


	// 
	// Always read in basecalls since they are used to check the sanity
	// of the alignment indices.
	//
	metricOptions["Basecall"] = true;
	
	//
	// Translate from the metrics to be loaded to the ones that are
	// required to compute them.
	//
	
	vector<string> datasetFields;
	RequirementMap fieldRequirements;
	BuildRequirementMap(fieldRequirements);
	StoreDatasetFieldsFromPulseFields(metricOptions, fieldRequirements, datasetFields);

	
	vector<string> movieFileNames;
	vector<string> fofnMovieNames;

	FileOfFileNames::StoreFileOrFileList(movieFileName, movieFileNames);

	HDFBasReader hdfBasReader;
	HDFPlsReader hdfPlsReader;
  HDFCCSReader<SMRTSequence> hdfCcsReader;

	vector<string> baseFileFields, pulseFileFields;
	int fieldIndex;

	bool useBaseFile = false, usePulseFile = false;

	for (fieldIndex = 0; fieldIndex < datasetFields.size(); fieldIndex++) {
		if (hdfBasReader.ContainsField(datasetFields[fieldIndex])) {
			useBaseFile = true;
			baseFileFields.push_back(datasetFields[fieldIndex]);
		}
	}

	if (maxElements != 0) {
		hdfBasReader.maxAllocNElements = maxElements;
		hdfPlsReader.maxAllocNElements = maxElements;
	}

	//
	// For now, all runs will attempt to use information from a .bas
	// file, since it's assumed that if one has alignments, one has a
	// .bas file.
	//
	useBaseFile = true;
	//
	// Add some default fields.
	//
	hdfBasReader.IncludeField("Basecall");
	hdfBasReader.IncludeField("PulseIndex");

  hdfBasReader.InitializeFields(baseFileFields);

  
	for (fieldIndex = 0; fieldIndex < datasetFields.size(); fieldIndex++) {
		if (hdfPlsReader.ContainsField(datasetFields[fieldIndex])) {
			usePulseFile = true;
			pulseFileFields.push_back(datasetFields[fieldIndex]);
		}
	}
	if (usePulseFile) {
		hdfPlsReader.InitializeFields(pulseFileFields);
	}
	hdfPlsReader.IncludeField("NumEvent");

		
	
	int nMovies = movieFileNames.size();
	int movieIndex;
	MovieNameToArrayIndex movieNameMap;
	//
	// Initialize movies. This accomplishes two tasks.  First, all movie
	// files are opened and initialized, so that if there are data
	// fields missing the program will exit now rather than in the
	// middle of loading pulses.  
	// Next, a list of movie names is created in fofnMovieNames.  The
	// cmp file does not necessarily index movies in the order of the
	// fofn, and so when loading pulses from a movie indexed by a cmp
	// file, one needs to look up the file name of the movie.  This is
	// done by scanning the fofnMovieNames list in order until the movie
	// is found. 

	for (movieIndex = 0; movieIndex < nMovies; movieIndex++) {

    if (!hdfBasReader.Initialize(movieFileNames[movieIndex])) {
      cout << "ERROR, could not initialize HDF file "
           << movieFileNames[movieIndex] << " for reading bases." << endl;
      exit(1);
    }
    else {
      fofnMovieNames.push_back(hdfBasReader.GetMovieName());
      movieNameMap[hdfBasReader.GetMovieName()] = movieIndex;
      hdfBasReader.Close();
    }

		// 
		// The pulse file is optional.  
		//
		if (usePulseFile) {
			if (hdfPlsReader.Initialize(movieFileNames[movieIndex]) == 0) {
				usePulseFile = false;
			}
		}		
	}

	CmpFile cmpFile;
	
	/*
	 * These readers pull information from the same pls file.
	 */
	HDFCmpFile<CmpAlignment> cmpReader;

	if (cmpReader.Initialize(cmpFileName, H5F_ACC_RDWR) == 0) {
		cout << "ERROR, could not open the cmp file." << endl;
		exit(0);
	}
	
  cmpReader.Read(cmpFile);

  string commandLine;
  clp.CommandLineToString(argc, argv, commandLine);
  string versionStr(VERSION);
  AppendPerforceChangelist(PERFORCE_VERSION_STRING, versionStr);
  cmpReader.fileLogGroup.AddEntry(commandLine, "Loading pulse metrics", "loadPulses", GetTimestamp(), versionStr);


	//
	// Group alignment indices by movie so that they may be processed one movie at a time
	// later on.  The movie indices set keeps track of all indices
	// listed in alignment files.  This keeps a reference to all
	// alignments in memory at once.   At the time of writing this, most
	// projects will have at most a few million alignments, and so the
	// size of this structure is modest.
	//

	UInt alignmentIndex;
	map<int, vector<int> > movieIndexSets;

	for (alignmentIndex = 0; alignmentIndex < cmpFile.alnInfo.alignments.size(); alignmentIndex++) {
		movieIndexSets[cmpFile.alnInfo.alignments[alignmentIndex].GetMovieId()].push_back(alignmentIndex);
	}

	vector<float>  computedPulseField;
	string   alignedSequence;
	string   readSequence;
	vector<unsigned char> byteAlignment;
	int m;
	vector<int> baseToAlignmentMap;

	//
	// Load pulses from movies in order they appear in the input fofn.
	//
  int fofnMovieIndex;
  for (fofnMovieIndex = 0; fofnMovieIndex < fofnMovieNames.size(); fofnMovieIndex++) {
    
    if (cmpFile.readType == ReadType::CCS or useCcs) {
      hdfBasReader.SetReadBasesFromCCS();
      hdfCcsReader.Initialize(movieFileNames[fofnMovieIndex]);
    }
    hdfBasReader.Initialize(movieFileNames[fofnMovieIndex]);
		BaseFile  baseFile;
		PulseFile pulseFile;

    if (byRead == false) {
      //
      // Read the entire bas file at once, and then extract values
      // from memory.  This can be faster depending on the chunk
      // size and size of the movie.
      //
      hdfBasReader.ReadBaseFile(baseFile);
      hdfBasReader.Close();
    }
    else {
      //
      // Reads are scanned one by instead of caching all.  It is
      // still necessary to read in some of the datasets entirely,
      // in particular the start positions and hole numbers.
      //


      // This is repeated below for a pulse file.  Since the pulse
      // and base files are separate objects, the scan data is
      // read into each separately.  Somehow later the information
      // should be merged into just one.
      if (hdfBasReader.scanDataReader.fileHasScanData) {
        hdfBasReader.scanDataReader.Read(baseFile.scanData);
      }
      baseFile.readStartPositions.resize(hdfBasReader.nReads+1);
      baseFile.readStartPositions[0] = 0;
      hdfBasReader.GetAllReadLengths(baseFile.readLengths);
      int i;
      assert(baseFile.readLengths.size() + 1 == baseFile.readStartPositions.size());
      for (i = 1; i < hdfBasReader.nReads + 1; i++ ) {
        baseFile.readStartPositions[i] = baseFile.readLengths[i-1] + baseFile.readStartPositions[i-1];
      }
      
      //
      // Although the whole bas file isn't being read in, it is
      // necessary to read in which hole numbers are contained in this
      // bas file since it is possible that the alignment for a
      // particular hole number may be in a different input bas.h5
      // file even if it is the same movie. 
      //
      hdfBasReader.GetAllHoleNumbers(baseFile.holeNumbers);
    }
    set<uint32_t> moviePartHoleNumbers;
    copy(baseFile.holeNumbers.begin(), baseFile.holeNumbers.end(), inserter(moviePartHoleNumbers, moviePartHoleNumbers.begin()));

		
		if (usePulseFile) {
			hdfPlsReader.Initialize(movieFileNames[fofnMovieIndex]);
			hdfPlsReader.IncludeField("NumEvent");
      hdfPlsReader.IncludeField("StartFrame");
      if (byRead == false) { 
        hdfPlsReader.ReadPulseFile(pulseFile);
        hdfPlsReader.Close();
      }
      else {
        if (usePulseFile) {
          pulseFile.pulseStartPositions.resize(hdfBasReader.nReads+1);
          pulseFile.pulseStartPositions[0] = 0;
          hdfPlsReader.GetAllNumEvent(pulseFile.numEvent);
          int i;
          for (i = 1; i < hdfBasReader.nReads + 1; i++ ) {
            pulseFile.pulseStartPositions[i] = pulseFile.numEvent[i-1] + pulseFile.pulseStartPositions[i-1];
          }
          if (hdfPlsReader.scanDataReader.fileHasScanData) {
            hdfPlsReader.scanDataReader.Read(pulseFile.scanData);
          }
        }
      }
		}

    string cmpFileMovieName;

    for (m = 0; m < cmpFile.movieInfo.name.size(); m++) {
      //
      // First find the file name for the movie 'm'
      //
      cmpFileMovieName = cmpFile.movieInfo.name[m];
      int fofnMovieIndex;
      
      if (baseFile.GetMovieName() == cmpFileMovieName) {
				break;
			}
		}

    //
    // If the movie specified in the input.fofn is not found in the
    // cmp file, that indicates something bad is happeing.  Either the
    // input.fofn was not used to generate the cmp.h5 file, or no
    // alignments were found between the input bas.h5 and the
    // reference.  That shouldn't happen.
    // 
		if (m == cmpFile.movieInfo.name.size()) {
			cout << "WARNING: The movie indexed in the compare file " << cmpFileMovieName << " is not listed in the file " << movieFileName << endl;
			continue;
		}
		
		//
		// Open the movie and load its pulses into memory.
		//
		movieIndex = cmpFile.movieInfo.id[m];
		int movieAlignmentIndex;
		float NaN = 0.0/0.0;
    
    UChar missingQualityValue = 255;
    HalfWord missingFrameRateValue    = USHRT_MAX;
    unsigned int missingPulseIndex = UINT_MAX;
    //
    // Since usePulseFile is set when the input file is a pulseFile,
    // and ReadType::CCS becomes the read type when the alignments are
    // ccs, when pulse files are specified for de novo ccs alignments,
    // they will be opened as pulse files.  Since the de novo ccs
    // sequences do not have pulse file information, the auto-reading
    // of pulse files needs to be disabled.  Do that here.
    //
    if (cmpFile.readType == ReadType::CCS or useCcs) {
      usePulseFile = false;
    }


		//
		// Now check the sanity of metric options.
		//

		map<string,bool>::iterator metricIt;
		for (metricIt = metricOptions.begin(); metricIt != metricOptions.end(); ++metricIt) {
			if (metricIt->second == false) {
				continue;
			}
			bool metricMayBeComputed = true;
      if (cmpFile.readType == ReadType::CCS and
          metricIt->first != "QualityValue"  and
          metricIt->first != "DeletionQV" and
          metricIt->first != "SubstitutionQV" and
          metricIt->first != "InsertionQV" and
          metricIt->first != "DeletionTag" and
          metricIt->first != "SubstitutionTag" and
          metricIt->first != "Basecall") {
        cout << "ERROR! The metric " << metricIt->first << " cannot be loaded into de novo ccs alignemnts." << endl;
        //        exit(0);
        metricMayBeComputed = false;
      }
      
			if (metricIt->first == "IPD") {
				//
				// The field requirements for IPD are special. 
				//
				if ((useBaseFile and !hdfBasReader.FieldIsIncluded("PreBaseFrames")) or
						(usePulseFile and (!hdfPlsReader.FieldIsIncluded("StartFrame") and
															 !hdfPlsReader.FieldIsIncluded("WidthInFrames")))) {
					metricMayBeComputed = false;
				}
			}
			else {
				if (fieldRequirements.find(metricIt->first) != fieldRequirements.end()) {
					//
					// There are requirements for this field. Make sure all are
					// present before trying to compute this field.
					//
					int requirementIndex;
					for (requirementIndex = 0; requirementIndex < fieldRequirements[metricIt->first].size(); ++requirementIndex) {
						string requirement;
						requirement = fieldRequirements[metricIt->first][requirementIndex];
				
						if (((useBaseFile == false or ((hdfBasReader.includedFields.find(requirement) == hdfBasReader.includedFields.end() or
 																						hdfBasReader.includedFields[requirement] == false))) and
								 ((usePulseFile == false or (hdfPlsReader.includedFields.find(requirement) == hdfPlsReader.includedFields.end() or
																						 hdfPlsReader.includedFields[requirement] == false))))) {
							metricMayBeComputed = false;
						}
					}
				}
				else {
					//
					// There are no requirements for this field, so it must exist as
					// a datset in either the bas or pls file.
					//
					if ((useBaseFile  == false or ((hdfBasReader.includedFields.find(metricIt->first) == hdfBasReader.includedFields.end() or
																					hdfBasReader.includedFields[metricIt->first] == false))) and
							(usePulseFile == false or (((hdfPlsReader.includedFields.find(metricIt->first) == hdfPlsReader.includedFields.end() or
																					 hdfPlsReader.includedFields[metricIt->first] == false))))) {
						metricMayBeComputed = false;
					}
				}
			}
			if (metricMayBeComputed == false) {
        if (failOnMissingData) {
          cout << "ERROR";
        }
        else {
          cout << "WARNING";
        }
        cout << ": There is insufficient data to compute metric: " << metricIt->first << " in the file " << movieFileNames[fofnMovieIndex] << " ";
        cout << " It will be ignored." << endl;
        if (failOnMissingData) {
          exit(1);
        }
				metricOptions[metricIt->first] = false;
			}
		}

		
		UInt i;
		//
		// This is currently used as a sentinal for showing that an array
		// element does not have a value stored for it, as in deleted
		// bases. 
		//

		
		vector<int> pulseIndexArray;
		vector<unsigned int> statTime;

		if (metricOptions["WhenStarted"]) {
			string whenStarted;
			if (hdfPlsReader.scanDataReader.useWhenStarted == false) {
				cout << "ERROR! Attempting to read WhenStarted from " 
						 << movieFileNames[fofnMovieIndex]
						 << " but the attriubte does not exist." << endl;
				exit(1);
			}
			hdfPlsReader.scanDataReader.ReadWhenStarted(whenStarted);
			
			if (!cmpReader.movieInfoGroup.whenStartedArray.IsInitialized()) {
				cmpReader.movieInfoGroup.whenStartedArray.Initialize(cmpReader.movieInfoGroup.movieInfoGroup, "WhenStarted");
			}

			cmpReader.movieInfoGroup.whenStartedArray.Write(&whenStarted, 1);
		}

    if (AnyFieldRequiresFrameRate(datasetFields)) {
      if (useBaseFile) {
        cmpReader.movieInfoGroup.StoreFrameRate(m, baseFile.GetFrameRate());
      }
      else if (usePulseFile) {
        cmpReader.movieInfoGroup.StoreFrameRate(m, pulseFile.GetFrameRate());
      }
    }
				
		//
		// An index set is a set of indices into the alignment array that
		// are of reads generated by this movie.  Load pulses for all
		// alignments generated for this movie.
		//

		//
		// Movie index sets should be sorted by alignment index. Build a lookup table for this.
		//
		
		std::vector<std::pair<int,int> > toFrom;
		for (movieAlignmentIndex = 0; movieAlignmentIndex < movieIndexSets[movieIndex].size(); movieAlignmentIndex++) {
			alignmentIndex = movieIndexSets[movieIndex][movieAlignmentIndex];
			toFrom.push_back(std::pair<int,int>(cmpFile.alnInfo.alignments[alignmentIndex].GetAlignmentId(), movieAlignmentIndex));
		}
		// orders by first by default.
		std::sort(toFrom.begin(), toFrom.end());

    //
    // Load metrics for alignments from movie 'movieIndex'.
    //
    cout << "loading " <<  movieIndexSets[movieIndex].size() << " alignments for movie " << movieIndex << endl;
		for (movieAlignmentIndex = 0; movieAlignmentIndex < movieIndexSets[movieIndex].size(); movieAlignmentIndex++) {
			alignmentIndex = movieIndexSets[movieIndex][toFrom[movieAlignmentIndex].second];


			//
			// Alignments are groupsd by ref group id then movie id.
			//
			int refGroupId  = cmpFile.alnInfo.alignments[alignmentIndex].GetRefGroupId();
			int movieId     = cmpFile.alnInfo.alignments[alignmentIndex].GetMovieId();
      UInt holeNumber = cmpFile.alnInfo.alignments[alignmentIndex].GetHoleNumber();

      //
      // Since the movie may be split into multiple parts, look to see
      // if this hole number is one of the ones covered by this
      // set. If it is not, just continue. It will be loaded on
      // another pass through a different movie part.
      //
      if (moviePartHoleNumbers.find(holeNumber) == moviePartHoleNumbers.end()) {
        continue;
      }

			//
			// Now locate where this movie is stored.
			//

			if (cmpReader.refGroupIdToArrayIndex.find(refGroupId) == cmpReader.refGroupIdToArrayIndex.end()) {
				cout << "ERROR!  An alignment " << alignmentIndex << " is specified with reference group " << endl
						 << refGroupId << " that is not found as an alignment group." << endl;
				exit(1);
			}
			int refGroupIndex = cmpReader.refGroupIdToArrayIndex[refGroupId];
			
			//
			// Now find the group containing the alignment for this movie.
			//
			if (cmpReader.refAlignGroups[refGroupIndex]->movieIdToIndex.find(movieId) ==
					cmpReader.refAlignGroups[refGroupIndex]->movieIdToIndex.end()) {
				cout << "ERROR!  An alignment " << alignmentIndex << " is specified with movie index " << endl
						 << movieId << " that is not found in the alignment group " << refGroupIndex << endl;
				exit(1);
			}

			int readGroupIndex = cmpReader.refAlignGroups[refGroupIndex]->movieIdToIndex[movieId];
      
			//
			// First do sanity check on the read to make sure the pules and the bases match.
			//

			//
			// Look to see if the output HDF arrays need to be created.
			//
			UInt offsetBegin, offsetEnd;
		
			offsetBegin = cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetBegin();
			offsetEnd   = cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetEnd();
		
			int alignedSequenceLength = offsetEnd - offsetBegin;
			if (alignedSequenceLength >= 0) {
				alignedSequence.resize(alignedSequenceLength);
				byteAlignment.resize(alignedSequenceLength);
			}
	
			//
			// Read the alignment string.  All alignments 
			//
			cmpReader.refAlignGroups[refGroupIndex]->readGroups[readGroupIndex]->alignmentArray.Read(offsetBegin, 
																																															 offsetEnd, 
																																															 &byteAlignment[0]);
		
			//
			// Convert to something we can compare easily.
			//
			ByteAlignmentToQueryString(&byteAlignment[0], byteAlignment.size(), &alignedSequence[0]);


			//
			// Do a sanity check to make sure the pulses and the alignment
			// make sense.  The main check is to see if the query sequence
			// in the alignment is the same as the query sequence in the
			// read. 
			//
		
			//
			// First pull out the bases corresponding to this read.
			//
			int queryStart = cmpFile.alnInfo.alignments[alignmentIndex].GetQueryStart();
			int queryEnd   = cmpFile.alnInfo.alignments[alignmentIndex].GetQueryEnd();

      // Build a map of where 
      CreateSequenceToAlignmentMap(byteAlignment, 
                                   baseToAlignmentMap);


			//
			// Condense gaps in the alignment for easy comparison.
			//
      //
      RemoveGaps(alignedSequence, alignedSequence);
      
			
			//
			// Query the cmp file for a way to look up a read based on
			// coordinate information.  For Astro reads, the coords are
			// based on x and y.  For Springfield, it is read index.  The
			// base files should be able to look up reads by x,y or by
			// index. 
			//
			int readIndex;

          
      if (cmpFile.platformId == Astro) {
        cout << "ASTRO pulse loading is deprecated." << endl;
        exit(0);
      }

      if (baseFile.LookupReadIndexByHoleNumber(holeNumber, readIndex) == false) {
          cout << "ERROR! Alignment has hole number " << holeNumber << " that is not in the movie. " << endl;
          assert(0);
      }

			int readStart, readLength, alignBaseStart, alignBaseEnd, alignBaseLength;
			readStart       = baseFile.readStartPositions[readIndex];
			readLength      = baseFile.readStartPositions[readIndex+1] - baseFile.readStartPositions[readIndex];
			alignBaseStart  = readStart + queryStart;
			alignBaseEnd    = readStart + queryEnd;
			alignBaseLength = alignBaseEnd - alignBaseStart;

			int pulseStart;
			if (usePulseFile) {
				pulseStart      = pulseFile.pulseStartPositions[readIndex];
			}

	    
      //
      // This maps from pulse to a base, since there are more pulses
      // called than bases, and the is one pulse for every base.
      //
			pulseIndexArray.resize(readLength);

      
      SMRTSequence sourceRead;
      unsigned int numPasses;
      //
      // These are not allocated in the regular allocate function
      // since they are only used in loadPulses. (maybe I should
      // subclass SMRTSequence here).
      //
      
      if (byRead) {
        // Read in the data from the bas file if it exsts.
        if (useBaseFile) {
          hdfBasReader.GetReadAt(readIndex, sourceRead);
          if (cmpFile.readType == ReadType::CCS or useCcs) {
            numPasses = hdfCcsReader.GetNumPasses(readIndex);
          }
        }
        // Read in the data from the pls file if it exists.
        if (usePulseFile) {
          hdfPlsReader.GetReadAt(readIndex, sourceRead.pulseIndex, sourceRead);
        }
      }
      else {
        //
        // The entire base/pulse file was read in, so copy data from that into a read
        // For the data used in the read, it is possible to simply
        // reference the data,  but for the pls file it is necessary
        // to copy since there is a packing of data.
        //
        if (useBaseFile) {
          baseFile.CopyReadAt(readIndex, sourceRead);
          if (cmpFile.readType == ReadType::CCS or useCcs) {
            numPasses = hdfCcsReader.GetNumPasses(readIndex);
          }
        }
        if (usePulseFile) {
          //
          // Copy the subset of pulses that correspond to the ones called as bases.
          //
          int i;
          for (i = 0; i < readLength; i++) {
            pulseIndexArray[i] = pulseStart + baseFile.pulseIndex[readStart + i];
          }
          pulseFile.CopyReadAt(readIndex, &pulseIndexArray[0], sourceRead);
        }
      }

      readSequence.resize(queryEnd - queryStart);
      CapQualityValues(sourceRead);
			copy((char*) (sourceRead.seq + queryStart),
					 (char*) (sourceRead.seq + queryEnd),
					 readSequence.begin());
      
			bool stringsMatch = true;
			if (alignedSequence.size() != readSequence.size() or alignedSequence != readSequence) {
				cout << "ERROR, the query sequence does not match the aligned query sequence." << endl;
				cout << "HoleNumber: "<< holeNumber << ", MovieName: " << cmpFileMovieName;
        cout << " ,ReadIndex: " << (int) readIndex << 
				cout << ", qStart: "<< queryStart << ", qEnd: " << queryEnd << endl;
				cout << "Aligned sequence: "<< endl;
				cout << alignedSequence << endl;
				cout << "Original sequence: " << endl;
				cout << readSequence << endl;
				assert(0);
      }

			/*
			 * Compute any necessary data fields.  These usually involve
			 * using differences of pulse indices, pulse widths, etc..
			 * Missing fields are stored as 0's. 
			 */

			vector<float> readPulseMetric;
            vector<float> floatMetric;
      vector<UChar> qvMetric;
      vector<HalfWord> frameRateMetric;
      vector<uint32_t> timeMetric;
			int ungappedAlignedSequenceLength = alignedSequence.size();
			
      floatMetric.resize(alignedSequenceLength+1);
      readPulseMetric.resize(alignedSequenceLength+1);
      qvMetric.resize(alignedSequenceLength+1);
      frameRateMetric.resize(alignedSequenceLength+1);
      timeMetric.resize(alignedSequenceLength+1);

			UInt i;
			UInt pi;

			HDFCmpExperimentGroup* expGroup = cmpReader.refAlignGroups[refGroupIndex]->readGroups[readGroupIndex];

      if (cmpFile.readType == ReadType::CCS or useCcs) {
        if (!cmpReader.alnInfoGroup.numPasses.IsInitialized()) {
          cmpReader.alnInfoGroup.InitializeNumPasses();
        }
        cmpReader.alnInfoGroup.numPasses.WriteToPos(&numPasses, 1, alignmentIndex);
      }
      
			if (metricOptions["StartTimeOffset"] == true) {
				if (!expGroup->startTimeOffset.IsInitialized()) {
					expGroup->startTimeOffset.Initialize(expGroup->experimentGroup, "StartTimeOffset");
				}
        unsigned int readStartTimeOffset = sourceRead.startFrame[queryStart];
				expGroup->startTimeOffset.WriteToPos(&readStartTimeOffset, 1, alignmentIndex);
			}

			if (metricOptions["QualityValue"] == true) {
				if (!expGroup->qualityValue.IsInitialized()) {
					expGroup->qualityValue.Initialize(expGroup->experimentGroup, "QualityValue");
				}
				
				// Store start time normalized to frame rate.
        fill(qvMetric.begin(), qvMetric.end(), missingQualityValue);

				for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
          qvMetric[baseToAlignmentMap[i]] = sourceRead.qual[queryStart + i];
        }
				qvMetric[qvMetric.size()-1] = 0;
				expGroup->qualityValue.WriteToPos(&qvMetric[0], qvMetric.size(), offsetBegin);
			}

			if (metricOptions["InsertionQV"] == true) {
				if (!expGroup->insertionQV.IsInitialized()) {
					expGroup->insertionQV.Initialize(expGroup->experimentGroup, "InsertionQV");
				}
				
				// Store start time normalized to frame rate.
        fill(qvMetric.begin(), qvMetric.end(), missingQualityValue);
				for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
          qvMetric[baseToAlignmentMap[i]] = sourceRead.insertionQV[queryStart+ i];
				}
				qvMetric[qvMetric.size()-1] = 0;
				expGroup->insertionQV.WriteToPos(&qvMetric[0], qvMetric.size(), offsetBegin);
			}

			if (metricOptions["MergeQV"] == true) {
				if (!expGroup->mergeQV.IsInitialized()) {
					expGroup->mergeQV.Initialize(expGroup->experimentGroup, "MergeQV");
				}
				
				// Store start time normalized to frame rate.
        fill(qvMetric.begin(), qvMetric.end(), missingQualityValue);
				for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
          qvMetric[baseToAlignmentMap[i]] = sourceRead.mergeQV[queryStart+ i];
				}
				qvMetric[qvMetric.size()-1] = 0;
				expGroup->mergeQV.WriteToPos(&qvMetric[0], qvMetric.size(), offsetBegin);
			}

			if (metricOptions["DeletionQV"] == true) {
				if (!expGroup->deletionQV.IsInitialized()) {
					expGroup->deletionQV.Initialize(expGroup->experimentGroup, "DeletionQV");
				}
				
				// Store start time normalized to frame rate.
        fill(qvMetric.begin(), qvMetric.end(), missingQualityValue);
				for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
          qvMetric[baseToAlignmentMap[i]] = sourceRead.deletionQV[queryStart+i];
				}
				qvMetric[qvMetric.size()-1] = 0;
				expGroup->deletionQV.WriteToPos(&qvMetric[0], qvMetric.size(), offsetBegin);
			}

			if (metricOptions["DeletionTag"] == true) {
				if (!expGroup->deletionTag.IsInitialized()) {
					expGroup->deletionTag.Initialize(expGroup->experimentGroup, "DeletionTag");
				}
        vector<char> readDeletionTagMetric;
        readDeletionTagMetric.resize(readPulseMetric.size());
				// Store start time normalized to frame rate.
				for (i = 0; i < readDeletionTagMetric.size()-1; i++ ) {
					readDeletionTagMetric[i] = '-';
				}
        readDeletionTagMetric[i] = '\0';
				for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
          assert(baseToAlignmentMap[i] < readDeletionTagMetric.size());
					readDeletionTagMetric[baseToAlignmentMap[i]] = sourceRead.deletionTag[queryStart+i];
				}
				readDeletionTagMetric[readDeletionTagMetric.size()-1] = 0;
				expGroup->deletionTag.WriteToPos(&readDeletionTagMetric[0], readDeletionTagMetric.size(), offsetBegin);
			}

			if (metricOptions["PulseIndex"] == true) {
        
				if (!expGroup->pulseIndex.IsInitialized()) {
					expGroup->pulseIndex.Initialize(expGroup->experimentGroup, "PulseIndex");
				}
				vector<uint32_t> readPulseIndexMetric;
        fill(readPulseIndexMetric.begin(), readPulseIndexMetric.end(), missingPulseIndex);
        readPulseIndexMetric.resize(readPulseMetric.size());
				// Store start time normalized to frame rate.
        assert(readPulseIndexMetric.size() > 0);
				for (i = 0; i < readPulseIndexMetric.size(); i++ ) {
          readPulseIndexMetric[i] = 0;
				}
				for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
					readPulseIndexMetric[baseToAlignmentMap[i]] = sourceRead.pulseIndex[queryStart+i];
				}
				readPulseIndexMetric[readPulseIndexMetric.size()-1] = 0;
				expGroup->pulseIndex.WriteToPos(&readPulseIndexMetric[0], readPulseIndexMetric.size(), offsetBegin);
			}

			if (metricOptions["SubstitutionTag"] == true) {
				if (!expGroup->substitutionTag.IsInitialized()) {
					expGroup->substitutionTag.Initialize(expGroup->experimentGroup, "SubstitutionTag");
				}
				vector<char> readSubstitutionTagMetric;
        readSubstitutionTagMetric.resize(readPulseMetric.size());
				// Store start time normalized to frame rate.
				for (i = 0; i < readSubstitutionTagMetric.size()-1; i++ ) {
          readSubstitutionTagMetric[i] = '-';
				}
        readSubstitutionTagMetric[i] = '\0';
				for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
					readSubstitutionTagMetric[baseToAlignmentMap[i]] = sourceRead.substitutionTag[queryStart+i];
				}
				readSubstitutionTagMetric[readSubstitutionTagMetric.size()-1] = 0;
				expGroup->substitutionTag.WriteToPos(&readSubstitutionTagMetric[0], readSubstitutionTagMetric.size(), offsetBegin);
      }

			if (metricOptions["SubstitutionQV"] == true) {
				if (!expGroup->substitutionQV.IsInitialized()) {
					expGroup->substitutionQV.Initialize(expGroup->experimentGroup, "SubstitutionQV");
				}
				
				// Store start time normalized to frame rate.
        fill(qvMetric.begin(), qvMetric.end(), missingQualityValue);

				for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
          qvMetric[baseToAlignmentMap[i]] = sourceRead.substitutionQV[queryStart+i];
				}
				qvMetric[qvMetric.size()-1] = 0;
				expGroup->substitutionQV.WriteToPos(&qvMetric[0], qvMetric.size(), offsetBegin);
			}

			if (metricOptions["ClassifierQV"] == true) {
				
				if (!expGroup->classifierQV.IsInitialized()) {
					expGroup->classifierQV.Initialize(expGroup->experimentGroup, "ClassifierQV");			
				}
				// Store start time normalized to frame rate.
        fill(floatMetric.begin(), floatMetric.end(), missingQualityValue);

				for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
					floatMetric[baseToAlignmentMap[i]] = sourceRead.classifierQV[i+queryStart];
				}
				floatMetric[floatMetric.size()-1] = 0;
				expGroup->classifierQV.WriteToPos(&floatMetric[0], floatMetric.size(), offsetBegin);
			}

			if (metricOptions["StartFrame"] == true) {
				if (!expGroup->startTime.IsInitialized()) {
					expGroup->startTime.Initialize(expGroup->experimentGroup, "StartFrame");			
				}

        if (useBaseFile) {
          sourceRead.startFrame = new unsigned int[sourceRead.length];
          copy(sourceRead.preBaseFrames, &sourceRead.preBaseFrames[sourceRead.length], sourceRead.startFrame);
          for (i = 0; i < sourceRead.length-1; i++) {
            sourceRead.startFrame[i+1] += sourceRead.widthInFrames[i];
          }
          partial_sum(sourceRead.startFrame, &sourceRead.startFrame[sourceRead.length],  sourceRead.startFrame);
        }
				
				// Store start time normalized to frame rate.
        fill(timeMetric.begin(), timeMetric.end(), missingPulseIndex);
				for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
					timeMetric[baseToAlignmentMap[i]] = sourceRead.startFrame[i+queryStart];
				}
				timeMetric[timeMetric.size()-1] = 0;
				expGroup->startTime.WriteToPos(&timeMetric[0], timeMetric.size(), offsetBegin);
			}

			if (metricOptions["PulseWidth"] == true) {
				if (!expGroup->pulseWidth.IsInitialized()) {
					expGroup->pulseWidth.Initialize(expGroup->experimentGroup, "PulseWidth");			
				}
				// Store start time normalized to frame rate.
        fill(frameRateMetric.begin(), frameRateMetric.end(), missingFrameRateValue);

        //
        // For legacy reasons, it's possible the width in frames is
        // stored in the bas file. If this is the case, use the width
        // in frames there.  Otherwise, use the width in frames stored
        // in the pls file.
        for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
          frameRateMetric[baseToAlignmentMap[i]] = sourceRead.widthInFrames[queryStart + i];
        }
				frameRateMetric[frameRateMetric.size()-1] = 0;
				expGroup->pulseWidth.WriteToPos(&frameRateMetric[0], frameRateMetric.size(), offsetBegin);
			}

			if (metricOptions["PreBaseFrames"] == true) {
				if (!expGroup->preBaseFrames.IsInitialized()) {
					expGroup->preBaseFrames.Initialize(expGroup->experimentGroup, "PreBaseFrames");
				}
				// Compute width in frames normalized to frame rate.
        fill(frameRateMetric.begin(), frameRateMetric.end(), missingFrameRateValue);
				for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
					frameRateMetric[baseToAlignmentMap[i]] = sourceRead.preBaseFrames[i+queryStart];
				}
				frameRateMetric[frameRateMetric.size()-1] = 0;
				expGroup->preBaseFrames.WriteToPos(&frameRateMetric[0], frameRateMetric.size(), offsetBegin);
			}

			if (metricOptions["WidthInFrames"] == true) {
				if (!expGroup->widthInFrames.IsInitialized()) {
					expGroup->widthInFrames.Initialize(expGroup->experimentGroup, "WidthInFrames");
				}
				// Compute width in frames normalized to frame rate.
        fill(frameRateMetric.begin(), frameRateMetric.end(), missingFrameRateValue);

				for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
					if (usePulseFile) {
						frameRateMetric[baseToAlignmentMap[i]] = sourceRead.widthInFrames[i+queryStart];
					}
					else {
						frameRateMetric[baseToAlignmentMap[i]] = sourceRead.widthInFrames[i+queryStart];
          }
				}
				frameRateMetric[frameRateMetric.size()-1] = 0;
				expGroup->widthInFrames.WriteToPos(&frameRateMetric[0], frameRateMetric.size(), offsetBegin);
			}

			if (metricOptions["pkmid"] == true) {

				if (!expGroup->pkmid.IsInitialized()) {
					expGroup->pkmid.Initialize(expGroup->experimentGroup, "pkmid");
				}

				for (i = 0; i < readPulseMetric.size(); i++ ) {
          readPulseMetric[i] = NaN;
				}
				
				for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
          readPulseMetric[baseToAlignmentMap[i]] = sourceRead.midSignal[i+queryStart];
        }
				readPulseMetric[readPulseMetric.size()-1] = 0;
				expGroup->pkmid.WriteToPos(&readPulseMetric[0], readPulseMetric.size(), offsetBegin);
			}

			if (metricOptions["IPD"] == true) {
				if (!expGroup->ipd.IsInitialized()) {
					expGroup->ipd.Initialize(expGroup->experimentGroup, "IPD");
				}
        fill(frameRateMetric.begin(), frameRateMetric.end(), missingFrameRateValue);				

				for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {

					//
					// The IPD is undefined for the first base in a read.
          //
					if (usePulseFile ) {
						if (queryStart == 0 and i == 0) {
              frameRateMetric[baseToAlignmentMap[i]] = 0;
						}
						else {
              frameRateMetric[baseToAlignmentMap[i]] = (sourceRead.startFrame[i+queryStart]  
                                                        - sourceRead.startFrame[i+queryStart-1]
                                                        - sourceRead.widthInFrames[i+queryStart-1]);
						}
					}
					else if (useBaseFile) {
            frameRateMetric[baseToAlignmentMap[i]] = sourceRead.preBaseFrames[i + queryStart];
					}
        }
				frameRateMetric[frameRateMetric.size()-1] = 0;
				expGroup->ipd.WriteToPos(&frameRateMetric[0], frameRateMetric.size(), offsetBegin);			
			}

			
			if (metricOptions["Light"] == true) {
				if (!expGroup->light.IsInitialized()) {
					expGroup->light.Initialize(expGroup->experimentGroup, "Light");
				}
        fill(frameRateMetric.begin(), frameRateMetric.end(), missingFrameRateValue);
				for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
          frameRateMetric[baseToAlignmentMap[i]] = sourceRead.meanSignal[i+queryStart];
          frameRateMetric[baseToAlignmentMap[i]] = (frameRateMetric[baseToAlignmentMap[i]] * 
                                                    sourceRead.widthInFrames[i+queryStart]);
				}
				frameRateMetric[frameRateMetric.size()-1] = 0;
				expGroup->light.WriteToPos(&frameRateMetric[0], frameRateMetric.size(), offsetBegin);			
			}
    
      sourceRead.Free();
      Free(sourceRead.meanSignal);
      Free(sourceRead.maxSignal);
      Free(sourceRead.midSignal);
      Free(sourceRead.startFrame);
      Free(sourceRead.classifierQV);
      Free(sourceRead.widthInFrames);
		}

    if (byRead == true) {
      if (useBaseFile) {
        hdfBasReader.Close();
      }
      if (cmpFile.readType == ReadType::CCS or useCcs) {
        hdfCcsReader.Close();
      }
      if (usePulseFile) {
        hdfPlsReader.Close();
      }
    }
	} // done loading movies


	cmpReader.Close();
}