//
// Collect region indices for either all region types, or just a few specific region types.
//
//
int CollectRegionIndices(SMRTSequence &read, RegionTable ®ionTable,
std::vector<int> ®ionIndices, RegionType *regionTypes,
int numRegionTypes) {
int regionLow, regionHigh;
int prevNumRegionIndices = regionIndices.size();
if (FindRegionIndices(read, ®ionTable, regionLow, regionHigh)) {
int i;
for (i = regionLow; i < regionHigh; i++) {
if (regionTypes == NULL) {
regionIndices.push_back(i);
}
else {
int t;
for (t = 0; t < numRegionTypes; t++) {
if (regionTable.GetType(i) == regionTypes[t]) {
regionIndices.push_back(i);
break;
}
}
}
}
}
return regionIndices.size() - prevNumRegionIndices;
}
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 FindRegionIndices(SMRTSequence &read, RegionTable *regionTablePtr,
int ®ionLowIndex, int ®ionHighIndex) {
return FindRegionIndices(read.zmwData.holeNumber,
regionTablePtr, regionLowIndex, regionHighIndex);
}
