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#ifndef READREADER_H_
#define READREADER_H_
#include<cstdio>
#include<cstring>
#include<cstdlib>
#include<iostream>
#include<cassert>
#include<fstream>
#include<vector>
#include "utils.h"
#include "SingleRead.h"
#include "SingleReadQ.h"
#include "PairedEndRead.h"
#include "PairedEndReadQ.h"
#include "ReadIndex.h"
template<class ReadType>
class ReadReader {
public:
ReadReader() { s = 0; indices = NULL; arr = NULL; hasPolyA = false; seedLen = -1; }
ReadReader(int s, char readFs[][STRLEN], bool hasPolyA = false, int seedLen = -1);
~ReadReader();
void setIndices(ReadIndex** indices) {
this->indices = indices;
}
bool locate(READ_INT_TYPE); // You should guarantee that indices exist and rid is valid, otherwise return false; If it fails, you should reset it manually!
void reset();
bool next(ReadType& read, int flags = 7) {
bool success = read.read(s, (std::istream**)arr, flags);
if (success && seedLen > 0) { read.calc_lq(hasPolyA, seedLen); }
return success;
}
private:
int s; // number of files
ReadIndex **indices;
std::ifstream** arr;
std::streampos *locations;
bool hasPolyA;
int seedLen;
};
template<class ReadType>
ReadReader<ReadType>::ReadReader(int s, char readFs[][STRLEN], bool hasPolyA, int seedLen) {
assert(s > 0);
this->s = s;
arr = new std::ifstream*[s];
locations = new std::streampos[s];
indices = NULL;
for (int i = 0; i < s; i++) {
arr[i] = new std::ifstream(readFs[i]);
if (!arr[i]->is_open()) { fprintf(stderr, "Cannot open %s! It may not exist.\n", readFs[i]); exit(-1); }
locations[i] = arr[i]->tellg();
}
this->hasPolyA = hasPolyA;
this->seedLen = seedLen;
}
template<class ReadType>
ReadReader<ReadType>::~ReadReader() {
indices = NULL;
if (arr != NULL) {
for (int i = 0; i < s; i++) {
arr[i]->close();
delete arr[i];
}
delete[] arr;
}
if (locations != NULL) {
delete[] locations;
}
}
template<class ReadType>
bool ReadReader<ReadType>::locate(READ_INT_TYPE rid) {
READ_INT_TYPE crid = -1;
ReadType read;
if (indices == NULL) return false;
//We should make sure that crid returned by each indices is the same
for (int i = 0; i < s; i++) {
READ_INT_TYPE val = indices[i]->locate(rid, *arr[i]);
if (i == 0) { crid = val; } else { assert(crid == val); }
}
assert(crid <= rid);
while (crid < rid && read.read(s, (std::istream**)arr, 0)) ++crid;
if (crid < rid) return false;
std::vector<std::streampos> tmp(s);
for (int i = 0; i < s; i++) { tmp[i] = arr[i]->tellg(); }
if (!read.read(s, (std::istream**)arr, 0)) return false;
for (int i = 0; i < s; i++) {
locations[i] = tmp[i];
arr[i]->seekg(locations[i]);
}
return true;
}
template<class ReadType>
void ReadReader<ReadType>::reset() {
for (int i = 0; i < s; i++) {
arr[i]->seekg(locations[i]);
}
}
#endif /* READREADER_H_ */
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