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
|
#pragma once
// -----------------------------------------------------------------------
// Phylogenetics
typedef struct bio·Node
{
string name;
string comment;
double dist;
double support;
int nchild;
int ndescendent;
struct bio·Node *parent;
struct bio·Node *child[2];
struct bio·Node *sibling;
} bio·Node;
error phylo·addchild(bio·Node *parent, bio·Node* child);
bool phylo·isleaf(bio·Node *node);
typedef struct bio·Tree
{
bio·Node *root;
} bio·Tree;
/* newick i/o */
bio·Tree bio·readnewick(io·Peeker stream, void*, mem·Allocator heap, void*);
error bio·writenewick(bio·Tree tree, io·Putter out, void*);
// -----------------------------------------------------------------------
// Sequences
/* i/o */
typedef struct bio·FastaReader bio·FastaReader;
typedef struct bio·FastqReader bio·FastqReader;
typedef struct bio·Seq
{
int len;
byte *name;
byte *s;
byte *q;
} bio·Seq;
bio·FastaReader *bio·openfasta(io·Reader stream, void *s, mem·Allocator heap, void *h);
error bio·readfasta(bio·FastaReader *rdr, bio·Seq *seq);
error bio·closefasta(bio·FastaReader *rdr);
bio·FastqReader *bio·openfastq(io·Reader stream, void *s, mem·Allocator heap, void *h);
error bio·readfastq(bio·FastqReader *rdr, bio·Seq *seq);
error bio·closefastq(bio·FastqReader *rdr);
/* alignment */
enum
{
aln·K = 20, // kmer size (k <= 32)
aln·L = 3, // number of kmers / hash
aln·N = 1000, // number of hashes
};
error aln·sketch(byte *seq, int l, uint64 *phi[aln·N], int *locs[aln·N]);
error aln·sort(int len, int l, uint64 *vals);
|
