int searchIndels(ControlState& currentState, unsigned NumBoxes, const SearchWindow& window )
{
static int Count_DI = 0;
static int Count_DI_Plus = 0;
static int Count_DI_Minus = 0;
unsigned CloseIndex, FarIndex;
std::vector<unsigned> DI[NumBoxes];
unsigned TempBoxIndex;
LOG_INFO(*logStream << "Searching deletion-insertions ... " << std::endl);
//UserDefinedSettings *userSettings = UserDefinedSettings::Instance();
for (unsigned ReadIndex = 0; ReadIndex < currentState.Reads_SR.size(); ReadIndex++) {
SPLIT_READ& currentRead = currentState.Reads_SR[ReadIndex];
if (currentRead.Used
|| currentRead.UP_Far.empty() || currentRead.FragName != currentRead.FarFragName) {
continue;
}
CloseIndex = currentRead.UP_Close.size() - 1;
FarIndex = currentRead.UP_Far.size() - 1;
if (currentRead.UP_Far[FarIndex].Mismatches + currentRead.UP_Close[CloseIndex].Mismatches
> (short) (1 + userSettings->Seq_Error_Rate * (currentRead.UP_Far[FarIndex].LengthStr + currentRead.UP_Close[CloseIndex].LengthStr))) {
continue;
}
if (currentRead.MatchedD == Plus) {
if (currentRead.UP_Far[FarIndex].Direction == Minus) {
if (currentRead.UP_Far[FarIndex].LengthStr + currentRead.UP_Close[CloseIndex].LengthStr < currentRead.getReadLength() &&
currentRead.UP_Far[FarIndex].LengthStr + currentRead.UP_Close[CloseIndex].LengthStr >= userSettings->Min_Num_Matched_Bases &&
currentRead.UP_Far[FarIndex].AbsLoc > currentRead.UP_Close[CloseIndex].AbsLoc + 1) {
currentRead.Left = currentRead.UP_Close[CloseIndex].AbsLoc - currentRead.UP_Close[CloseIndex].LengthStr + 1;
currentRead.Right = currentRead.UP_Far[FarIndex].AbsLoc + currentRead.UP_Far[FarIndex].LengthStr - 1;
currentRead.BP = currentRead.UP_Close[CloseIndex].LengthStr - 1;
currentRead.NT_size = currentRead.getReadLength() - currentRead.UP_Far[FarIndex].LengthStr - currentRead.UP_Close[CloseIndex].LengthStr;
currentRead.NT_str = ReverseComplement( currentRead. getUnmatchedSeq()). substr( currentRead.BP + 1, currentRead.NT_size);
currentRead.IndelSize = (currentRead.Right - currentRead.Left) + currentRead.NT_size - currentRead.getReadLengthMinus();
currentRead.BPLeft = currentRead.UP_Close[CloseIndex].AbsLoc - g_SpacerBeforeAfter;
currentRead.BPRight = currentRead.UP_Far[FarIndex].AbsLoc - g_SpacerBeforeAfter;
if (1) {
if (readTransgressesBinBoundaries( currentRead, window.getEnd())) {
saveReadForNextCycle(currentRead, currentState.FutureReads_SR);
} else {
if (readInSpecifiedRegion( currentRead, userSettings->getRegion() ) ) {
TempBoxIndex = (int) (currentRead. BPLeft) / BoxSize;
if (TempBoxIndex < NumBoxes) {
DI[TempBoxIndex]. push_back(ReadIndex);
currentRead.Used = true;
Count_DI++;
Count_DI_Plus++;
}
}
}
}
}
}
} else if (currentRead.MatchedD == Minus) {
if (currentRead.UP_Far[FarIndex].Direction == Plus) {
if (currentRead.UP_Close[CloseIndex].LengthStr + currentRead.UP_Far[FarIndex].LengthStr < currentRead.getReadLength() &&
currentRead.UP_Close[CloseIndex].LengthStr + currentRead.UP_Far[FarIndex].LengthStr >= userSettings->Min_Num_Matched_Bases &&
currentRead.UP_Close[CloseIndex].AbsLoc > currentRead.UP_Far[FarIndex].AbsLoc + 1) {
currentRead.Left = currentRead.UP_Far[FarIndex].AbsLoc - currentRead.UP_Far[FarIndex].LengthStr + 1;
currentRead.Right = currentRead.UP_Close[CloseIndex].AbsLoc + currentRead.UP_Close[CloseIndex].LengthStr - 1;
currentRead.BP = currentRead.UP_Far[FarIndex].LengthStr - 1;
currentRead.NT_size = currentRead.getReadLength() - currentRead.UP_Close[CloseIndex].LengthStr - currentRead.UP_Far[FarIndex].LengthStr;
currentRead.NT_str = currentRead.getUnmatchedSeq(). substr( currentRead.BP + 1, currentRead.NT_size);
currentRead.IndelSize = (currentRead.Right - currentRead.Left) - currentRead.getReadLengthMinus() + currentRead.NT_size;
currentRead.BPLeft = currentRead.UP_Far[FarIndex].AbsLoc - g_SpacerBeforeAfter;
currentRead.BPRight = currentRead.UP_Close[CloseIndex].AbsLoc - g_SpacerBeforeAfter;
{
if ( 1 ) {
if (readTransgressesBinBoundaries( currentRead, window.getEnd())) {
saveReadForNextCycle( currentRead, currentState.FutureReads_SR);
} else {
if (readInSpecifiedRegion( currentRead, userSettings->getRegion())) {
TempBoxIndex = (int) (currentRead. BPLeft) / BoxSize;
if (TempBoxIndex < NumBoxes) {
DI[TempBoxIndex]. push_back(ReadIndex);
currentRead.Used = true;
Count_DI++;
Count_DI_Minus++;
}
}
}
}
}
}
}
}
}
LOG_INFO(*logStream << "Total: " << Count_DI << "\t+" << Count_DI_Plus << "\t-"
<< Count_DI_Minus << std::endl);
std::ofstream DeletionOutf( userSettings->getDOutputFilename().c_str(), std::ios::app);
std::ofstream inversionsOutf( userSettings->getINVOutputFilename().c_str(), std::ios::app);
SortOutputDI(currentState, NumBoxes, window.getChromosome()->getSeq(), currentState.Reads_SR, DI, DeletionOutf, inversionsOutf);
DeletionOutf.close();
for (unsigned int i = 0; i < NumBoxes; i++) {
DI[i].clear();
}
return EXIT_SUCCESS;
}
void SearchDeletions::outputResults(BDData & g_bdData, ControlState& currentState, std::vector<unsigned> Vars[], const unsigned NumBoxes, const SearchWindow& currentWindow)
{
std::ofstream DeletionOutf(UserDefinedSettings::Instance()->getDOutputFilename().c_str(), std::ios::app);
SortOutputD(currentState, NumBoxes, currentWindow.getChromosome()->getSeq(), currentState.Reads_SR, Vars, DeletionOutf);
DeletionOutf.close();
}