gkmer.h

/*
The MIT License (MIT)

Copyright (c) 2024 Hanfc <h2624366594@gmail.com>

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

*/

#ifndef GKMER_H
#define GKMER_H

#define YAK_MAX_KMER     31
#define YAK_COUNTER_BITS 10
#define YAK_N_COUNTS     (1<<YAK_COUNTER_BITS)
#define YAK_MAX_COUNT    ((1<<YAK_COUNTER_BITS)-1)

#define YAK_BLK_SHIFT  9 // 64 bytes, the size of a cache line
#define YAK_BLK_MASK   ((1<<(YAK_BLK_SHIFT)) - 1)

#define yak_ch_eq(a, b) ((a)>>YAK_COUNTER_BITS == (b)>>YAK_COUNTER_BITS) // lower 8 bits for counts; higher bits for k-mer
#define yak_ch_hash(a) ((a)>>YAK_COUNTER_BITS)

#include <stdint.h>

typedef struct {
	int32_t bf_shift, bf_n_hash;
	int32_t k;
	int32_t pre;
	int32_t n_thread;
	int64_t chunk_size;
} yak_copt_t;

void yak_copt_init(yak_copt_t *o);
void gkmerAPI(yak_copt_t *opt, const char *inf, char *histo);

#endif // GKMER_H