diff options
Diffstat (limited to 'include/libbio.h')
| -rw-r--r-- | include/libbio.h | 31 |
1 files changed, 9 insertions, 22 deletions
diff --git a/include/libbio.h b/include/libbio.h index f802e22..7b28a55 100644 --- a/include/libbio.h +++ b/include/libbio.h @@ -52,32 +52,19 @@ 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·SeqReader bio·SeqReader; +typedef struct bio·SeqWriter bio·SeqWriter; typedef struct bio·Seq { int len; - byte *name; - byte *s; - byte *q; + char *name; + char *s; + char *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·SeqReader *bio·open(io·Reader io, void *rdr, mem·Allocator mem, void *heap); +error bio·close(bio·SeqReader *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 = 10, // 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); +error bio·readfasta(bio·SeqReader *rdr, bio·Seq *seq); +error bio·readfastq(bio·SeqReader *rdr, bio·Seq *seq); |