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A fix for unsigned value subtract problem #84

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A fix for unsigned value subtract problem #84

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12 changes: 6 additions & 6 deletions src/bddata.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -119,7 +119,7 @@ void BDData::loadBDFile(const std::string& filename)

firstPos += g_SpacerBeforeAfter; // ??? ask Kai
secondPos += g_SpacerBeforeAfter;
if (firstChrName == secondChrName && secondChrName != "" && abs(firstPos - secondPos) < 500) {
if (firstChrName == secondChrName && secondChrName != "" && abs((long long int) firstPos - (long long int) secondPos) < 500) {
continue;
}
if ( firstChrName!="" && secondChrName!="") {
Expand Down Expand Up @@ -180,16 +180,16 @@ void SortRPByChrPos(std::vector <RP_READ> & Reads_RP) { // no interchromosome RP
bool RecipicalOverlap(RP_READ & first, RP_READ & second)
{
int distance = 1000;
if (abs(first.PosA - first.PosA1) > distance) {
if (abs((long long int) first.PosA - (long long int) first.PosA1) > distance) {
return false;
}
if (abs(first.PosB - first.PosB1) > distance) {
if (abs((long long int) first.PosB - (long long int) first.PosB1) > distance) {
return false;
}
if (abs(second.PosA - second.PosA1) > distance) {
if (abs((long long int) second.PosA - (long long int) second.PosA1) > distance) {
return false;
}
if (abs(second.PosB - second.PosB1) > distance) {
if (abs((long long int) second.PosB - (long long int) second.PosB1) > distance) {
return false;
}
float cutoff = 0.9;
Expand Down Expand Up @@ -424,7 +424,7 @@ void ModifyRP(std::vector <RP_READ> & Reads_RP)
Reads_RP[first].PosB = Reads_RP[first].PosB + Reads_RP[first].ReadLength;
Reads_RP[first].PosB1 = Reads_RP[first].PosB1 + Reads_RP[first].ReadLength;
}
if (Reads_RP[first].ChrNameA == Reads_RP[first].ChrNameB && abs(Reads_RP[first].PosA - Reads_RP[first].PosB) < 500) {
if (Reads_RP[first].ChrNameA == Reads_RP[first].ChrNameB && abs((long long int) Reads_RP[first].PosA - (long long int) Reads_RP[first].PosB) < 500) {
Reads_RP[first].Visited = true;
}
//std::cout << "Final: " << Reads_RP[first].ChrNameA << " " << Reads_RP[first].DA << " " << Reads_RP[first].PosA << "\t" << Reads_RP[first].ChrNameB << " " << Reads_RP[first].DB << " " << Reads_RP[first].PosB << std::endl;
Expand Down
2 changes: 1 addition & 1 deletion src/genotyping.cpp
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Expand Up @@ -124,7 +124,7 @@ void doGenotyping (ControlState & CurrentState, UserDefinedSettings* userSetting
// step 4 for each variant, do genotyping
for (unsigned SV_index =0; SV_index < AllSV4Genotyping.size(); SV_index++) {
// step 4.1 if type == DEL, GenotypeDel
if (AllSV4Genotyping[SV_index].ChrA == AllSV4Genotyping[SV_index].ChrB && abs(AllSV4Genotyping[SV_index].PosA - AllSV4Genotyping[SV_index].PosB) < SV_Genotype_Cutoff) {
if (AllSV4Genotyping[SV_index].ChrA == AllSV4Genotyping[SV_index].ChrB && abs((long long int) AllSV4Genotyping[SV_index].PosA - (long long int) AllSV4Genotyping[SV_index].PosB) < SV_Genotype_Cutoff) {
std::cout << "Skip One SV " << OneSV.Type << " " << OneSV.ChrA << " " << OneSV.PosA << " "
<< OneSV.CI_A << " " << OneSV.ChrB << " " << OneSV.PosB << " "
<< OneSV.CI_B << std::endl;
Expand Down
2 changes: 1 addition & 1 deletion src/pindel.cpp
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Expand Up @@ -1554,7 +1554,7 @@ void MergeInterChr(ControlState& currentState, UserDefinedSettings *usersettings
continue;
}
if (All[index_a].FirstChrName == All[index_b].FirstChrName && All[index_a].SecondChrName == All[index_b].SecondChrName) {
if (abs(All[index_a].FirstPos - All[index_b].FirstPos) < 10 && abs(All[index_a].SecondPos - All[index_b].SecondPos) < 10 && All[index_a].NumSupport + All[index_b].NumSupport >= cutoff) {
if (abs((long long int) All[index_a].FirstPos - (long long int) All[index_b].FirstPos) < 10 && abs((long long int) (All[index_a].SecondPos - All[index_b].SecondPos)) < 10 && All[index_a].NumSupport + All[index_b].NumSupport >= cutoff) {

INToutputfile << "chr\t" << All[index_a].FirstChrName << "\tpos\t" << unsigned((All[index_a].FirstPos + All[index_b].FirstPos) / 2) << "\tchr\t" << All[index_a].SecondChrName << "\tpos\t"
<< unsigned((All[index_a].SecondPos + All[index_b].SecondPos) / 2) << "\tseq\t" << All[index_a].InsertedSequence << "\tsupport\t" << All[index_a].NumSupport + All[index_b].NumSupport << "\tINFOR\t"
Expand Down