int Initialize(string ccsBasFileName,
const H5::FileAccPropList & fileAccPropList = H5::FileAccPropList::DEFAULT) {
//
// Open the file and initialize for reading reads.
//
//
// First, initialize for reading the unrolled bases from this
// file.
//
if (this->T_HDFBasReader<T_Sequence>::Initialize(ccsBasFileName, fileAccPropList) == 0) {
cout << "ERROR, Could not initialize ccs file " << ccsBasFileName << endl;
exit(1);
}
if (this->pulseDataGroup.ContainsObject("ConsensusBaseCalls") and
ccsGroup.Initialize(this->hdfBasFile, "PulseData/ConsensusBaseCalls") == 0) {
cout << "ERROR, attempting to read cicular consensus data from '" << ccsBasFileName
<< "', which does not contain a ConsensusBaseCalls field." << endl;
cout << "Check HDF file structure." << endl;
exit(1);
}
curPassPos = 0;
int passesSuccess = 1;
if (ccsGroup.ContainsObject("Passes") == 0) {
passesSuccess = 0;
}
else {
if (passesGroup.Initialize(ccsGroup.group,"Passes") == 0) {
passesSuccess = 0;
}
}
if (passesSuccess == 0) {
cout <<"ERROR, attempting to read circular consensus group Passes but it does not exist. " << endl;
cout <<"Check HDF file structure."<<endl;
exit(1);
}
//
// Initialize the bas reader to read ccs reads as normal bas reads.
//
// Next, the location of the bases is in a non-standard group.
ccsBasReader.baseCallsGroupName = "ConsensusBaseCalls";
//
// Read in the CCS fields that are the same as the base fields,
// but in a different group.
//
// ccsBasReader.OpenHDFFile(ccsBasFileName);
//
// Initialize the fields that are read.
//
ccsBasReader.IncludeField("Basecall");
ccsBasReader.IncludeField("InsertionQV");
ccsBasReader.IncludeField("DeletionQV");
ccsBasReader.IncludeField("DeletionTag");
ccsBasReader.IncludeField("SubstitutionQV");
ccsBasReader.IncludeField("SubstitutionTag");
ccsBasReader.IncludeField("QualityValue");
//
// Initialize this without opening a file.
//
ccsBasReader.Initialize(&this->rootGroup);
//ccsBasReader.InitializeForReadingPulseInformation();
//ccsBasReader.LoadRunInfo();
/*
* Initialize pass information for reading.
*/
if (this->InitializeField(passesGroup, "AdapterHitAfter", adapterHitAfterArray, this->includedFields["AdapterHitAfter"]) == 0) return 0;
if (this->InitializeField(passesGroup, "AdapterHitBefore", adapterHitBeforeArray, this->includedFields["AdapterHitBefore"]) == 0) return 0;
if (this->InitializeField(passesGroup, "NumPasses", numPassesArray, this->includedFields["NumPasses"]) == 0) return 0;
if (this->InitializeField(passesGroup, "PassDirection", passDirectionArray, this->includedFields["PassDirection"]) == 0) return 0;
if (this->InitializeField(passesGroup, "PassNumBases", passNumBasesArray, this->includedFields["PassNumBases"]) == 0) return 0;
if (this->InitializeField(passesGroup, "PassStartBase", passStartBaseArray, this->includedFields["PassStartBase"]) == 0) return 0;
//
// The following two fields are not critical.
//
this->InitializeField(passesGroup, "PassStartPulse", passStartPulseArray, this->includedFields["PassStartPulse"]);
this->InitializeField(passesGroup, "PassNumPulses", passNumPulsesArray, this->includedFields["PassNumPulses"]);
//
// The zmw reader contains the group that hols all pass information
//
zmwReader.Initialize(&ccsBasReader.baseCallsGroup);
return 1;
}
int main(int argc, char* argv[]) {
string inFileName, outFileName;
if (argc < 3) {
PrintUsage();
exit(1);
}
inFileName = argv[1];
outFileName = argv[2];
vector<int> readIndices;
int argi = 3;
vector<string> patterns;
vector<int> holeNumbers;
string regionTableFileName = "";
int from = 0, to = 0;
while (argi < argc) {
if (strlen(argv[argi]) > 0 and argv[argi][0] == '-'){
if (strcmp(argv[argi], "-pat") == 0) {
patterns.push_back(argv[++argi]);
}
else if (strcmp(argv[argi], "-holenumber") == 0) {
holeNumbers.push_back(atoi(argv[++argi]));
}
else if (strcmp(argv[argi], "-regionTable") == 0) {
regionTableFileName = argv[++argi];
}
else if (strcmp(argv[argi], "-fromto") == 0) {
from = atoi(argv[++argi]);
to = atoi(argv[++argi]);
if (from >= to) {
cout <<"ERROR. From must be less than to." << endl;
exit(0);
}
}
else {
cout <<"Error. Bad option " << argv[argi] << endl;
PrintUsage();
exit(1);
}
}
else {
readIndices.push_back(atoi(argv[argi]));
}
++argi;
}
int index;
for (index = from; index < to; index++) {
readIndices.push_back(index);
}
std::sort(readIndices.begin(), readIndices.end());
T_HDFBasReader<SMRTSequence> reader;
HDFRegionTableReader regionReader;
HDFBasWriter writer;
HDFRegionTableWriter regionWriter;
reader.InitializeDefaultIncludedFields();
writer.InitializeDefaultIncludedFields();
writer.IncludeField("HoleNumber");
writer.IncludeField("HoleXY");
vector<string> inFiles;
FileOfFileNames::StoreFileOrFileList(inFileName, inFiles);
inFileName = inFiles[0];
reader.Initialize(inFileName);
RegionTable regionTable;
if (regionTableFileName != "") {
regionReader.Initialize(regionTableFileName);
}
else {
regionReader.Initialize(inFileName);
}
regionReader.ReadTable(regionTable);
string changeListID;
reader.GetChangeListID(changeListID);
if (reader.scanDataReader.GetPlatformId() == AstroPlatform) {
writer.Initialize(outFileName, reader.GetMovieName(), reader.GetRunCode());
}
else {
writer.Initialize(outFileName, reader.GetMovieName(), changeListID);
}
regionWriter.Initialize(writer.pulseDataGroup);
int ri;
int curReadIndex = 0;
SMRTSequence seq;
bool printSeq = false;
ri = 0;
if (readIndices.size() > 0) {
reader.PrepareForRandomAccess();
for (ri = 0; ri < readIndices.size(); ri++) {
reader.GetReadAt(readIndices[ri], seq);
writer.Write(seq);
//
// Write out region information for the read.
//
int low, high;
FindRegionIndices(readIndices[ri], ®ionTable, low, high);
int regionIndex;
for (regionIndex = low; regionIndex < high; regionIndex++) {
regionWriter.Write(regionTable.table[regionIndex]);
}
}
regionWriter.Finalize(regionTable.columnNames,
regionTable.regionTypes,
regionTable.regionDescriptions,
regionTable.regionSources
);
}
else if (patterns.size() > 0) {
while (reader.GetNext(seq)) {
printSeq = false;
if (curReadIndex < readIndices.size() and ri == readIndices[curReadIndex]) {
++curReadIndex;
printSeq = true;
}
int p;
for (p = 0; p < patterns.size(); p++) {
if (ExactPatternMatch(seq.title, patterns[p])) {
printSeq = true;
break;
}
}
for (p = 0; p < holeNumbers.size(); p++) {
if (seq.holeNumber == holeNumbers[p]) {
printSeq = true;
break;
}
}
if (printSeq) {
cout << "writing " << seq.title << endl;
writer.Write(seq);
}
++ri;
}
}
writer.Flush();
}
int GetNext(T_Sequence &ccsSequence) {
//
// Read in all ccs pass data.
//
ccsSequence.Free();
int retVal = 0;
if (this->curRead == ccsBasReader.nReads) {
return 0;
}
if (this->curBasePos == ccsBasReader.nBases) {
return 0;
}
try {
UInt numPasses;
numPassesArray.Read(this->curRead, this->curRead+1, &numPasses);
if (numPasses > 0) {
// Read in the ccs bases
if ((retVal = ccsBasReader.GetNext((SMRTSequence&)ccsSequence)) == 0)
return 0;
ccsSequence.numPasses = numPasses;
if (this->includedFields["AdapterHitAfter"]) {
ccsSequence.adapterHitAfter.resize(ccsSequence.numPasses);
adapterHitAfterArray.Read(curPassPos, curPassPos + ccsSequence.numPasses, &ccsSequence.adapterHitAfter[0]);
}
if (this->includedFields["AdapterHitBefore"]) {
ccsSequence.adapterHitBefore.resize(ccsSequence.numPasses);
adapterHitBeforeArray.Read(curPassPos, curPassPos + ccsSequence.numPasses, &ccsSequence.adapterHitBefore[0]);
}
if (this->includedFields["PassDirection"]) {
ccsSequence.passDirection.resize(ccsSequence.numPasses);
passDirectionArray.Read(curPassPos, curPassPos + ccsSequence.numPasses, &ccsSequence.passDirection[0]);
}
if (this->includedFields["PassNumBases"]) {
ccsSequence.passNumBases.resize(ccsSequence.numPasses);
passNumBasesArray.Read(curPassPos, curPassPos + ccsSequence.numPasses, &ccsSequence.passNumBases[0]);
}
if (this->includedFields["PassStartBase"]) {
ccsSequence.passStartBase.resize(ccsSequence.numPasses);
passStartBaseArray.Read(curPassPos, curPassPos + ccsSequence.numPasses, &ccsSequence.passStartBase[0]);
}
if (this->includedFields["PassStartPulse"]) {
ccsSequence.passStartPulse.resize(ccsSequence.numPasses);
passStartPulseArray.Read(curPassPos, curPassPos + ccsSequence.numPasses, &ccsSequence.passStartPulse[0]);
}
if (this->includedFields["PassNumPulses"]) {
ccsSequence.passNumPulses.resize(ccsSequence.numPasses);
passNumPulsesArray.Read(curPassPos, curPassPos + ccsSequence.numPasses, &ccsSequence.passNumPulses[0]);
}
curPassPos += ccsSequence.numPasses;
}
else {
// advance a read in the ccs sequence without advancing positions.
ccsBasReader.curRead++;
}
//
// Regardless whether or not a ccs read was called, read the next
// unrolled read, since an unrolled read is called for each zmw.
//
retVal = ((T_HDFBasReader<SMRTSequence>*)this)->GetNext(ccsSequence.unrolledRead);
ccsSequence.zmwData = ccsSequence.unrolledRead.zmwData;
ccsSequence.CopyTitle(ccsSequence.unrolledRead.title);
string newTitle = string(ccsSequence.title) + string("/ccs");
ccsSequence.CopyTitle(newTitle.c_str());
} catch (H5::DataSetIException e) {
cout << "ERROR, could not read ccs data for CCS Sequence "
<< ccsSequence.unrolledRead.title << endl;
exit(1);
}
// cout << "title: " << ccsSequence.title << endl;
if (retVal == 0) {
return 0;
}
else {
return 1;
}
}
