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#pragma once
// -----------------------------------------------------------------------
// Phylogenetics
typedef struct bio·Node
{
string name;
string comment;
double dist;
double support;
int nnode;
int nchild;
struct bio·Node *parent;
struct bio·Node *sibling;
struct bio·Node *child;
} bio·Node;
typedef struct bio·Tree
{
bio·Node *root;
int nleaf;
mem·Allocator heap;
void *h;
} bio·Tree;
// clade functions
error phylo·addchild(bio·Node* parent, bio·Node* child);
error phylo·rmchild(bio·Node* parent, bio·Node* child);
error phylo·countnodes(bio·Node *node, int *n);
error phylo·countleafs(bio·Node *node, int *n);
error phylo·ladderize(bio·Node *root);
/* newick i/o */
error bio·readnewick(io·Peeker stream, void*, bio·Tree* tree);
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(uintptr len, int l, uint64 *vals);
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