int main(int argc, char* argv[]) {
string basFileName;
if (argc < 2) {
cout << "usage: bas2 file.bas.h5 " << endl;
cout << "bas2 = bas ls" << endl;
cout << " -t --titleindices Print the titles of reads and their indices in the file." << endl;
}
basFileName = argv[1];
int argi = 1;
bool printSummary = true;
bool printTitleIndices = false;
while (argi < argc) {
if (strcmp(argv[argi], "-t") == 0 or
strcmp(argv[argi], "--titleindices") == 0) {
printTitleIndices = true;
printSummary = false;
}
++argi;
}
HDFBasReader reader;
reader.Initialize(basFileName);
int numReads = reader.GetNumReads();
cout << "Num reads: " << numReads << endl;
vector<int> readLengths;
reader.GetAllReadLengths(readLengths);
DNALength totalLength = 0;
VectorIndex i;
int numAbove100 = 0;
for (i = 0; i< readLengths.size(); i++ ){
totalLength += readLengths[i];
if (readLengths[i] > 100) {
++numAbove100;
}
}
if (printSummary) {
if (numReads > 0 ){
cout << "Average read length: " << totalLength / (1.0*numReads) << endl;
}
cout << "A total of " << numAbove100 << " have length > 100" << endl;
return 0;
}
if (printTitleIndices) {
FASTQSequence seq;
int seqIndex = 0;
while (reader.GetNext(seq)) {
cout << seqIndex << " " << seq.title << " " << seq.length << endl;
++seqIndex;
}
}
}
int main(int argc, char* argv[]) {
string inFileName, outFileName;
if (argc < 3) {
cout << "usage: filterHDFPls in out idx1 [idx2 idx3]..." << endl;
exit(1);
}
inFileName = argv[1];
outFileName = argv[2];
vector<int> readIndices;
int argi = 3;
int minLength = 0;
int minAvgQual = 0;
while (argi < argc) {
if (strcmp(argv[argi], "-minLength") == 0) {
minLength = atoi(argv[++argi]);
}
else if (strcmp(argv[argi], "-minAvgQual") == 0) {
minAvgQual = atoi(argv[++argi]);
}
++argi;
}
std::sort(readIndices.begin(), readIndices.end());
HDFBasReader reader;
HDFBasWriter writer;
reader.Initialize(inFileName);
writer.Initialize(outFileName, reader.GetMovieName(), reader.GetRunCode());
int ri;
int curReadIndex = 0;
FASTQSequence seq;
for (ri = 0; ri < readIndices.size(); ri++, curReadIndex++ ){
reader.GetNext(seq);
bool skipRead = false;
if (seq.length < minLength) { skipRead = true;}
if (seq.GetAverageQuality() < minAvgQual) { skipRead = true; }
if (skipRead) { continue; }
// all ok, write read out.
writer.Write(seq);
}
}
TEST(SubreadsTest, EndToEnd_Multiple)
{
// setup
const string movieName = "m140905_042212_sidney_c100564852550000001823085912221377_s1_X0";
vector<string> baxFilenames;
baxFilenames.push_back(tests::Data_Dir + "/" + movieName + ".1.bax.h5");
const string generatedBam = movieName + ".subreads.bam";
const string scrapBam = movieName + ".scraps.bam";
// run conversion
const int result = RunBax2Bam(baxFilenames, "--subread");
EXPECT_EQ(0, result);
// open BAX reader on original data
HDFBasReader baxReader;
baxReader.IncludeField("Basecall");
baxReader.IncludeField("DeletionQV");
baxReader.IncludeField("DeletionTag");
baxReader.IncludeField("InsertionQV");
baxReader.IncludeField("PreBaseFrames");
baxReader.IncludeField("MergeQV");
baxReader.IncludeField("SubstitutionQV");
baxReader.IncludeField("HQRegionSNR");
// not using SubTag or PulseWidth here
string baxBasecallerVersion;
string baxBindingKit;
string baxSequencingKit;
const int initOk = baxReader.Initialize(baxFilenames.front());
EXPECT_EQ(1, initOk);
if (initOk == 1) {
if (baxReader.scanDataReader.fileHasScanData && baxReader.scanDataReader.initializedRunInfoGroup) {
if (baxReader.scanDataReader.runInfoGroup.ContainsAttribute("BindingKit")) {
HDFAtom<std::string> bkAtom;
if (bkAtom.Initialize(baxReader.scanDataReader.runInfoGroup, "BindingKit")) {
bkAtom.Read(baxBindingKit);
bkAtom.dataspace.close();
}
}
if (baxReader.scanDataReader.runInfoGroup.ContainsAttribute("SequencingKit")) {
HDFAtom<std::string> skAtom;
if (skAtom.Initialize(baxReader.scanDataReader.runInfoGroup, "SequencingKit")) {
skAtom.Read(baxSequencingKit);
skAtom.dataspace.close();
}
}
}
baxReader.GetChangeListID(baxBasecallerVersion);
}
// read region table info
boost::scoped_ptr<HDFRegionTableReader> regionTableReader(new HDFRegionTableReader);
RegionTable regionTable;
std::string fn = baxFilenames.front();
EXPECT_TRUE(regionTableReader->Initialize(fn) != 0);
regionTable.Reset();
regionTableReader->ReadTable(regionTable);
regionTableReader->Close();
EXPECT_NO_THROW(
{
// open BAM file
BamFile bamFile(generatedBam);
// check BAM header information
const BamHeader& header = bamFile.Header();
EXPECT_EQ(string("1.5"), header.Version());
EXPECT_EQ(string("unknown"), header.SortOrder());
EXPECT_EQ(string("3.0.1"), header.PacBioBamVersion());
EXPECT_TRUE(header.Sequences().empty());
EXPECT_TRUE(header.Comments().empty());
ASSERT_FALSE(header.Programs().empty());
const vector<string> readGroupIds = header.ReadGroupIds();
ASSERT_FALSE(readGroupIds.empty());
const ReadGroupInfo& rg = header.ReadGroup(readGroupIds.front());
string rawId = movieName + "//SUBREAD";
string md5Id;
MakeMD5(rawId, md5Id, 8);
EXPECT_EQ(md5Id, rg.Id());
EXPECT_EQ(string("PACBIO"), rg.Platform());
EXPECT_EQ(movieName, rg.MovieName());
EXPECT_TRUE(rg.SequencingCenter().empty());
EXPECT_TRUE(rg.Date().empty());
EXPECT_TRUE(rg.FlowOrder().empty());
EXPECT_TRUE(rg.KeySequence().empty());
EXPECT_TRUE(rg.Library().empty());
EXPECT_TRUE(rg.Programs().empty());
EXPECT_TRUE(rg.PredictedInsertSize().empty());
EXPECT_TRUE(rg.Sample().empty());
EXPECT_EQ("SUBREAD", rg.ReadType());
EXPECT_EQ(baxBasecallerVersion, rg.BasecallerVersion());
EXPECT_EQ(baxBindingKit, rg.BindingKit());
EXPECT_EQ(baxSequencingKit, rg.SequencingKit());
EXPECT_EQ(75, std::stod(rg.FrameRateHz()));
EXPECT_EQ("dq", rg.BaseFeatureTag(BaseFeature::DELETION_QV));
EXPECT_EQ("dt", rg.BaseFeatureTag(BaseFeature::DELETION_TAG));
EXPECT_EQ("iq", rg.BaseFeatureTag(BaseFeature::INSERTION_QV));
EXPECT_EQ("ip", rg.BaseFeatureTag(BaseFeature::IPD));
EXPECT_EQ("mq", rg.BaseFeatureTag(BaseFeature::MERGE_QV));
EXPECT_EQ("sq", rg.BaseFeatureTag(BaseFeature::SUBSTITUTION_QV));
EXPECT_FALSE(rg.HasBaseFeature(BaseFeature::SUBSTITUTION_TAG));
EXPECT_EQ(FrameCodec::V1, rg.IpdCodec());
// compare 1st record from each file
SMRTSequence baxRecord;
UInt holeNumber = 0;
vector<float> hqSnr;
size_t intervalIdx = 0;
vector<SubreadInterval> subreadIntervals;
size_t numTested = 0;
EntireFileQuery entireFile(bamFile);
for (BamRecord& bamRecord : entireFile) {
if (intervalIdx >= subreadIntervals.size())
{
while (baxReader.GetNext(baxRecord))
{
holeNumber = baxRecord.zmwData.holeNumber;
ComputeSubreadIntervals(&subreadIntervals, regionTable, holeNumber);
/* this is for debugging subread interval problems
int hqStart = 0;
int hqEnd = 0;
int hqScore = 0;
LookupHQRegion(holeNumber,
regionTable,
hqStart,
hqEnd,
hqScore);
vector<ReadInterval> subreadIntervals_;
CollectSubreadIntervals(baxRecord, ®ionTable, subreadIntervals_);
for (int i = subreadIntervals_.size() - 1; i >= 0; --i)
{
auto& in = subreadIntervals_[i];
int inStart = max(hqStart, in.start);
int inEnd = min(hqEnd, in.end);
if (inEnd <= inStart)
subreadIntervals_.erase(subreadIntervals_.begin() + i);
}
cerr << "hqRegion: " << hqStart << ", " << hqEnd << endl;
cerr << "subreadRegions:" << endl;
for (const auto& in : subreadIntervals_)
cerr << " l, r: " << in.start << ", " << in.end << endl;
cerr << "adapterDerived:" << endl;
for (const auto& in : subreadIntervals)
cerr << " l, r: " << in.Start << ", " << in.End << endl;
cerr << endl;
// */
if (subreadIntervals.empty())
continue;
intervalIdx = 0;
hqSnr.clear();
hqSnr.push_back(baxRecord.HQRegionSnr('A'));
hqSnr.push_back(baxRecord.HQRegionSnr('C'));
hqSnr.push_back(baxRecord.HQRegionSnr('G'));
hqSnr.push_back(baxRecord.HQRegionSnr('T'));
EXPECT_GT(hqSnr[0], 0);
EXPECT_GT(hqSnr[1], 0);
EXPECT_GT(hqSnr[2], 0);
EXPECT_GT(hqSnr[3], 0);
goto compare;
}
goto cleanup;
}
compare:
const BamRecordImpl& bamRecordImpl = bamRecord.Impl();
EXPECT_EQ(4680,bamRecordImpl.Bin());
EXPECT_EQ(0, bamRecordImpl.InsertSize());
EXPECT_EQ(255, bamRecordImpl.MapQuality());
EXPECT_EQ(-1, bamRecordImpl.MatePosition());
EXPECT_EQ(-1, bamRecordImpl.MateReferenceId());
EXPECT_EQ(-1, bamRecordImpl.Position());
EXPECT_EQ(-1, bamRecordImpl.ReferenceId());
EXPECT_FALSE(bamRecordImpl.IsMapped());
const int subreadStart = subreadIntervals[intervalIdx].Start;
const int subreadEnd = subreadIntervals[intervalIdx].End;
const string expectedName = movieName + "/" +
to_string(holeNumber) + "/" +
to_string(subreadStart) + "_" +
to_string(subreadEnd);
EXPECT_EQ(expectedName, bamRecordImpl.Name());
using PacBio::BAM::QualityValue;
using PacBio::BAM::QualityValues;
const DNALength length = subreadEnd - subreadStart;
string expectedSequence;
expectedSequence.assign((const char*)baxRecord.seq + subreadStart, length);
const string bamSequence = bamRecord.Sequence();
const QualityValues bamQualities = bamRecord.Qualities();
EXPECT_EQ(expectedSequence, bamSequence);
EXPECT_TRUE(bamQualities.empty());
const QualityValues bamDeletionQVs = bamRecord.DeletionQV();
const QualityValues bamInsertionQVs = bamRecord.InsertionQV();
const QualityValues bamMergeQVs = bamRecord.MergeQV();
const QualityValues bamSubstitutionQVs = bamRecord.SubstitutionQV();
for (size_t i = 0; i < length; ++i) {
const size_t pos = subreadStart + i;
EXPECT_EQ((QualityValue)baxRecord.GetDeletionQV(pos), bamDeletionQVs.at(i));
EXPECT_EQ((QualityValue)baxRecord.GetInsertionQV(pos), bamInsertionQVs.at(i));
EXPECT_EQ((QualityValue)baxRecord.GetMergeQV(pos), bamMergeQVs.at(i));
EXPECT_EQ((QualityValue)baxRecord.GetSubstitutionQV(pos), bamSubstitutionQVs.at(i));
}
if (baxRecord.deletionTag)
{
string expectedDeletionTags;
expectedDeletionTags.assign((char*)baxRecord.deletionTag + subreadStart,
(char*)baxRecord.deletionTag + subreadStart + length);
const string& bamDeletionTags = bamRecord.DeletionTag();
EXPECT_EQ(expectedDeletionTags, bamDeletionTags);
}
if (baxRecord.substitutionTag)
{
string expectedSubstitutionTags;
expectedSubstitutionTags.assign((char*)baxRecord.substitutionTag + subreadStart,
(char*)baxRecord.substitutionTag + subreadStart + length);
const string& bamSubstitutionTags = bamRecord.SubstitutionTag();
EXPECT_EQ(expectedSubstitutionTags, bamSubstitutionTags);
}
// TODO: IPDs
const LocalContextFlags ctxFlags = subreadIntervals[intervalIdx].LocalContextFlags;
EXPECT_EQ(md5Id, bamRecord.ReadGroupId());
EXPECT_EQ(movieName, bamRecord.MovieName());
EXPECT_EQ(1, bamRecord.NumPasses());
EXPECT_EQ(holeNumber, bamRecord.HoleNumber());
EXPECT_EQ(subreadStart, bamRecord.QueryStart());
EXPECT_EQ(subreadEnd, bamRecord.QueryEnd());
EXPECT_EQ(hqSnr, bamRecord.SignalToNoise());
EXPECT_EQ(ctxFlags, bamRecord.LocalContextFlags());
numTested++;
intervalIdx++;
}
cleanup:
EXPECT_GT(numTested, 1);
// cleanup
baxReader.Close();
RemoveFile(generatedBam);
RemoveFile(scrapBam);
}); // EXPECT_NO_THROW
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", ®ionsFOFNName, "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, ®ionTable, 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;
}