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
|
#include <seqan/store.h>
using namespace seqan2;
int main()
{
//![store]
FragmentStore<> store;
//![store]
//![typedefs]
typedef FragmentStore<> TStore;
typedef Value<TStore::TAnnotationStore>::Type TAnnotation;
typedef TAnnotation::TId TId;
typedef TAnnotation::TId TPos;
typedef IntervalAndCargo<TPos, TId> TInterval;
//![typedefs]
//![interval]
String<String<TInterval> > intervals;
//![interval]
//![resize]
resize(intervals, length(store.contigStore));
//![resize]
//![tree]
typedef IntervalTree<TPos, TId> TIntervalTree;
String<TIntervalTree> intervalTrees;
//![tree]
//![resize_tree]
resize(intervals, length(store.contigStore));
//![resize_tree]
//![reads]
String<unsigned> readsPerGene;
//![reads]
//![read_alignment_type]
typedef Value<TStore::TAlignedReadStore>::Type TAlignedRead;
//![read_alignment_type]
TAlignedRead tmp; // sp no unused-Variable warning is triggered
//![resize_reads]
resize(readsPerGene, length(store.annotationStore), 0);
//![resize_reads]
//![result]
String<TId> result;
//![result]
return 0;
}
|
