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#include "soloInputFeatureUMI.h"
#include "SoloReadFeature.h"
#include "binarySearch2.h"
bool soloInputFeatureUMI(fstream *strIn, int32 featureType, bool readInfoYes, array<vector<uint64>,2> &sjAll, uint64 &iread,
int32 &cbmatch, uint32 &feature, uint64 &umi, vector<uint32> &featVecU32, SoloReadFlagClass &readFlagCounts)
{
if (!(*strIn >> umi)) //end of file
return false;
if (readInfoYes) {
*strIn >> iread >> readFlagCounts.flag;
};
switch (featureType) {
case SoloFeatureTypes::Gene :
case SoloFeatureTypes::GeneFull :
case SoloFeatureTypes::GeneFull_Ex50pAS :
case SoloFeatureTypes::GeneFull_ExonOverIntron :
*strIn >> feature;
break;
case SoloFeatureTypes::SJ :
uint64 sj[2];
*strIn >> sj[0] >> sj[1];
feature=(uint32) binarySearch2(sj[0],sj[1],sjAll[0].data(),sjAll[1].data(),sjAll[0].size());
break;
case SoloFeatureTypes::Transcript3p :
feature=0;
uint32 ntr, in1;
*strIn >> ntr;
featVecU32.resize(2*ntr);
for (uint32 ii=0; ii<2*ntr; ii++) {
*strIn >> in1;
featVecU32[ii]=in1;
};
break;
};
*strIn >> cbmatch;
return true;
};
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