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/* Copyright (C) 2013 Ion Torrent Systems, Inc. All Rights Reserved */
/* Author: Alex Artyomenko <aartyomenko@cs.gsu.edu> */
#ifndef ION_ANALYSIS_ORDEREDBAMWRITER_H
#define ION_ANALYSIS_ORDEREDBAMWRITER_H
#include <deque>
#include <queue>
#include <algorithm>
#include "BAMWalkerEngine.h"
using namespace std;
class Alignment;
template<typename T>
int cmp(T p1, T p2) { return p1 < p2 ? 1 : (p1 > p2 ? -1 : 0); }
template<typename T1, typename T2>
int cmp_pairs(T1 p11, T2 p12, T1 p21, T2 p22) { int lvl1 = cmp(p11, p21); if (lvl1) return lvl1; return cmp(p12, p22); }
struct AlignmentComporator {
bool operator()(Alignment* lhs, Alignment* rhs);
};
typedef priority_queue<Alignment*, deque<Alignment*>, AlignmentComporator> alignment_queue;
class OrderedBAMWriter : protected alignment_queue {
AlignmentComporator cmp;
public:
OrderedBAMWriter() : alignment_queue(cmp) { }
Alignment* process_new_etries(Alignment* list);
Alignment* flush();
private:
Alignment* wrap_items_in_linkedlist(Alignment * current);
bool cond(Alignment* current);
};
#endif //ION_ANALYSIS_ORDEREDBAMWRITER_H
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