-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathhashmapindex.h
58 lines (54 loc) · 3.34 KB
/
hashmapindex.h
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
/* Philip T.L.C. Clausen Jan 2017 [email protected] */
/*
* Copyright (c) 2017, Philip Clausen, Technical University of Denmark
* All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
#define _XOPEN_SOURCE 600
#include <stdio.h>
#ifndef HASHMAPINDEX
typedef struct hashMap_index HashMap_index;
struct hashMap_index {
unsigned len; // seqlen
unsigned size; // size of index
int *index; // k-mer posititions in seq
long unsigned *seq; // 2-bit sequence
unsigned kmerindex;
};
#define HASHMAPINDEX 1
#endif
/* pointers determining how indexes a stored */
extern void (*destroyPtr)(HashMap_index *);
extern HashMap_index * (*alignLoadPtr)(HashMap_index *, int, int, int, int, long unsigned, long unsigned);
int hashMap_index_initialize(HashMap_index *dest, int len, int kmerindex);
void hashMap_index_set(HashMap_index *dest);
void hashMap_index_destroy(HashMap_index *dest);
int hashMap_index_get(const HashMap_index *dest, long unsigned key, unsigned shifter);
int hashMap_index_get_bound(const HashMap_index *dest, long unsigned key, int min, int max, unsigned shifter);
int hashMap_index_getDubPos(const HashMap_index *dest, long unsigned key, int value, unsigned shifter);
int hashMap_index_getNextDubPos(const HashMap_index *dest, long unsigned key, int min, int max, unsigned index, unsigned shifter);
void hashMap_index_add(HashMap_index *dest, long unsigned key, int newpos, unsigned shifter);
void hashMapIndex_add(HashMap_index *dest, long unsigned key, int newpos);
HashMap_index * hashMap_index_load(HashMap_index *src, int seq, int index, int len, int kmersize);
void hashMap_index_dump(HashMap_index *src, FILE *seq, FILE *index);
HashMap_index * hashMap_index_build(HashMap_index *src, int seq, int len, int kmersize);
HashMap_index * alignLoad_fly(HashMap_index *dest, int seq_in, int index_in, int len, int kmersize, long unsigned seq_index, long unsigned index_index);
HashMap_index * alignLoad_fly_mem(HashMap_index *dest, int seq_in, int index_in, int len, int kmersize, long unsigned seq_index, long unsigned index_index);
HashMap_index * alignLoad_fly_build(HashMap_index *dest, int seq_in, int index_in, int len, int kmersize, long unsigned seq_index, long unsigned index_index);
HashMap_index * alignLoad_fly_build_mem(HashMap_index *dest, int seq_in, int index_in, int len, int kmersize, long unsigned seq_index, long unsigned index_index);
HashMap_index * alignLoad_skip(HashMap_index *dest, int seq_in, int index_in, int len, int kmersize, long unsigned seq_index, long unsigned index_index);
HashMap_index * alignLoad_fly_shm(HashMap_index *dest, int seq_in, int index_in, int len, int kmersize, long unsigned seq_index, long unsigned index_index);
HashMap_index * alignLoad_shm_initial(char *templatefilename, int file_len, int seq_in, int index_in, int kmersize);
void alignClean(HashMap_index *template_index);
void alignClean_shm(HashMap_index *template_index);