-
Notifications
You must be signed in to change notification settings - Fork 240
/
extsort.c
250 lines (220 loc) · 7.76 KB
/
extsort.c
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
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
/* ext-sort.h -- sort on disk
Copyright (C) 2020-2021 Genome Research Ltd.
Author: Petr Danecek <pd3@sanger.ac.uk>
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.
*/
#include <stdio.h>
#include <unistd.h> // for unlink()
#include <sys/stat.h> // for chmod()
#include <assert.h>
#include <fcntl.h>
#ifdef _WIN32
#include <windows.h>
#endif
#include "bcftools.h"
#include "extsort.h"
#include "kheap.h"
typedef struct
{
extsort_t *es; // this is to get access to extsort_cmp_f from kheap
int fd;
char *fname;
void *dat;
}
blk_t;
static inline int blk_is_smaller(blk_t **aptr, blk_t **bptr);
KHEAP_INIT(blk, blk_t*, blk_is_smaller) /* defines khp_blk_t */
struct _extsort_t
{
size_t dat_size, mem, max_mem;
char *tmp_prefix;
extsort_cmp_f cmp;
size_t nbuf, mbuf, nblk;
blk_t **blk;
void **buf, *tmp_dat;
khp_blk_t *bhp;
};
static inline int blk_is_smaller(blk_t **aptr, blk_t **bptr)
{
blk_t *a = *aptr;
blk_t *b = *bptr;
int ret = a->es->cmp(&a->dat,&b->dat);
if ( ret < 0 ) return 1;
return 0;
}
size_t parse_mem_string(const char *str);
void extsort_set(extsort_t *es, extsort_opt_t key, void *value)
{
if ( key==DAT_SIZE ) { es->dat_size = *((size_t*)value); return; }
if ( key==MAX_MEM )
{
es->max_mem = parse_mem_string(*((const char**)value));
if ( es->max_mem <=0 ) error("Could not parse the memory string, expected positive number: %s\n",*((const char**)value));
return;
}
if ( key==TMP_PREFIX ) { es->tmp_prefix = init_tmp_prefix(*((const char**)value)); return; }
if ( key==FUNC_CMP ) { es->cmp = *((extsort_cmp_f*)value); return; }
}
extsort_t *extsort_alloc(void)
{
extsort_t *es = (extsort_t*) calloc(1,sizeof(*es));
es->max_mem = 100e6;
return es;
}
void extsort_init(extsort_t *es)
{
assert( es->cmp );
assert( es->dat_size );
if ( !es->tmp_prefix ) es->tmp_prefix = init_tmp_prefix(NULL);
es->tmp_dat = malloc(es->dat_size);
}
void extsort_destroy(extsort_t *es)
{
int i;
for (i=0; i<es->nblk; i++)
{
blk_t *blk = es->blk[i];
if ( blk->fd!=-1 )
#ifdef _WIN32
_close(blk->fd);
#else
close(blk->fd);
#endif
free(blk->fname);
free(blk->dat);
free(blk);
}
free(es->tmp_dat);
free(es->tmp_prefix);
free(es->blk);
khp_destroy(blk, es->bhp);
free(es);
}
static void _buf_flush(extsort_t *es)
{
int i;
if ( !es->nbuf ) return;
qsort(es->buf, es->nbuf, sizeof(void*), es->cmp);
es->nblk++;
es->blk = (blk_t**) realloc(es->blk, sizeof(blk_t*)*es->nblk);
es->blk[es->nblk-1] = (blk_t*) calloc(1,sizeof(blk_t));
blk_t *blk = es->blk[es->nblk-1];
blk->es = es;
blk->dat = malloc(es->dat_size);
blk->fname = strdup(es->tmp_prefix);
#ifdef _WIN32
for (i=0; i<100000; i++)
{
memcpy(blk->fname,es->tmp_prefix,strlen(es->tmp_prefix));
mktemp(blk->fname);
blk->fd = _open(blk->fname, O_RDWR|O_CREAT|O_EXCL|O_BINARY|O_TEMPORARY, 0600);
if ( blk->fd==-1 )
{
if ( errno==EEXIST ) continue;
error("Error: failed to open a temporary file %s\n",blk->fname);
}
break;
}
if ( !blk->fd ) error("Error: failed to create a unique temporary file name from %s\n",es->tmp_prefix);
if ( _chmod(blk->fname, S_IRUSR|S_IWUSR)!=0 ) error("Error: failed to set permissions of the temporary file %s\n",blk->fname);
#else
if ( (blk->fd = mkstemp(blk->fname))==-1 )
error("Error: failed to open a temporary file %s\n",blk->fname);
if ( fchmod(blk->fd,S_IRUSR|S_IWUSR)!=0 ) error("Error: failed to set permissions of the temporary file %s\n",blk->fname);
unlink(blk->fname); // should auto delete when closed on linux, the descriptor remains open
#endif
for (i=0; i<es->nbuf; i++)
{
#ifdef _WIN32
if ( _write(blk->fd, es->buf[i], es->dat_size)!=es->dat_size ) error("Error: failed to write %zu bytes to the temporary file %s\n",es->dat_size,blk->fname);
#else
if ( write(blk->fd, es->buf[i], es->dat_size)!=es->dat_size ) error("Error: failed to write %zu bytes to the temporary file %s\n",es->dat_size,blk->fname);
#endif
free(es->buf[i]);
}
#ifdef _WIN32
if ( _lseek(blk->fd,0,SEEK_SET)!=0 ) error("Error: failed to lseek() to the start of the temporary file %s\n", blk->fname);
#else
if ( lseek(blk->fd,0,SEEK_SET)!=0 ) error("Error: failed to lseek() to the start of the temporary file %s\n", blk->fname);
#endif
es->nbuf = 0;
es->mem = 0;
}
void extsort_push(extsort_t *es, void *dat)
{
int delta = sizeof(void*) + es->dat_size;
if ( es->nbuf && es->mem + delta > es->max_mem ) _buf_flush(es);
es->nbuf++;
es->mem += delta;
hts_expand(void*, es->nbuf, es->mbuf, es->buf);
es->buf[es->nbuf-1] = dat;
}
// return number of elements read
static ssize_t _blk_read(extsort_t *es, blk_t *blk)
{
ssize_t ret = 0;
if ( blk->fd==-1 ) return ret;
#ifdef _WIN32
ret = _read(blk->fd, blk->dat, es->dat_size);
#else
ret = read(blk->fd, blk->dat, es->dat_size);
#endif
if ( ret < 0 ) error("Error: failed to read from the temporary file %s\n", blk->fname);
if ( ret == 0 )
{
#ifdef _WIN32
if ( _close(blk->fd)!=0 ) error("Error: failed to close the temporary file %s\n", blk->fname);
#else
if ( close(blk->fd)!=0 ) error("Error: failed to close the temporary file %s\n", blk->fname);
#endif
blk->fd = -1;
return ret;
}
if ( ret < es->dat_size ) error("Error: failed to read %zu bytes from the temporary file %s\n",es->dat_size,blk->fname);
return ret;
}
void extsort_sort(extsort_t *es)
{
_buf_flush(es);
free(es->buf);
es->buf = NULL;
es->bhp = khp_init(blk);
// open all blocks, read one record from each, create a heap
int i;
for (i=0; i<es->nblk; i++)
{
blk_t *blk = es->blk[i];
#ifdef _WIN32
if ( _lseek(blk->fd,0,SEEK_SET)!=0 ) error("Error: failed to lseek() to the start of the temporary file %s\n", blk->fname);
#else
if ( lseek(blk->fd,0,SEEK_SET)!=0 ) error("Error: failed to lseek() to the start of the temporary file %s\n", blk->fname);
#endif
int ret = _blk_read(es, blk);
if ( ret ) khp_insert(blk, es->bhp, &blk);
}
}
void *extsort_shift(extsort_t *es)
{
if ( !es->bhp->ndat ) return NULL;
blk_t *blk = es->bhp->dat[0];
// swap the pointer which keeps the location of user data so that it is not overwritten by the next read
void *tmp = es->tmp_dat; es->tmp_dat = blk->dat; blk->dat = tmp;
khp_delete(blk, es->bhp);
int ret = _blk_read(es, blk);
if ( ret ) khp_insert(blk, es->bhp, &blk);
return es->tmp_dat;
}