1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
|
/* Copyright (C) 2013 Ion Torrent Systems, Inc. All Rights Reserved */
/* Author: Alex Artyomenko <aartyomenko@cs.gsu.edu> */
#include "OrderedBAMWriter.h"
bool alignment_left_after_right (Alignment *lhs, Alignment *rhs)
{
if (lhs == rhs)
return false;
if (!rhs->processed)
return false;
if (!lhs->processed)
return true;
if (!rhs->alignment.IsMapped())
return false;
if (!lhs->alignment.IsMapped())
return true;
if (lhs->alignment.RefID > rhs->alignment.RefID)
return true;
if (lhs->alignment.RefID < rhs->alignment.RefID)
return false;
return lhs->alignment.Position > rhs->alignment.Position;
}
bool AlignmentComporator::operator()(Alignment *lhs, Alignment *rhs) {
return alignment_left_after_right(lhs, rhs);
}
bool OrderedBAMWriter::cond(Alignment *current) {
if (!current)
return !empty();
if (current == top())
return false;
if (!top()->processed)
return false;
if (!current->processed)
return true;
if (!top()->alignment.IsMapped())
return false;
if (!current->alignment.IsMapped())
return true;
if (current->alignment.RefID > top()->alignment.RefID)
return true;
if (current->alignment.RefID < top()->alignment.RefID)
return false;
return current->original_position > top()->alignment.Position;
/*
return current ? 1 == cmp_pairs(top()->alignment.RefID, top()->alignment.Position,
current->alignment.RefID, current->original_position) : !empty();
*/
}
Alignment* OrderedBAMWriter::process_new_etries(Alignment *list) {
if (!list) return NULL;
Alignment * last = list;
for (Alignment* current = list;current; last = current, current = current->next) {
push(current);
}
return wrap_items_in_linkedlist(last);
}
Alignment* OrderedBAMWriter::flush() {
return wrap_items_in_linkedlist(NULL);
}
Alignment* OrderedBAMWriter::wrap_items_in_linkedlist(Alignment * current) {
if (empty()) return NULL;
Alignment* result = NULL, *c = top();
while (cond(current)) {
if (!result) result = top();
c = top();
pop();
c->next = top();
}
if (result) c->next = NULL;
return result;
}
|
