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
|
/*************************************************************************************
The MIT License
BWA-MEM2 (Sequence alignment using Burrows-Wheeler Transform),
Copyright (C) 2019 Intel Corporation, Heng Li.
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.
Authors: Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@intel.com>.
*****************************************************************************************/
#include<stdio.h>
#include<stdlib.h>
#include<stdint.h>
#include "FMI_search.h"
#include <omp.h>
#include <string.h>
#ifdef VTUNE_ANALYSIS
#include <ittnotify.h>
#endif
#define QUERY_DB_SIZE 512000000
int myrank, num_ranks;
int main(int argc, char **argv) {
#ifdef VTUNE_ANALYSIS
__itt_pause();
#endif
if(argc!=7)
{
printf("Need seven arguments : ref_file query_set batch_size readlength minSeedLen max_mem_intv\n");
return 1;
}
int32_t numReads = 0;
int64_t total_size = 0;
gzFile fp = gzopen(argv[2], "r");
if (fp == 0)
{
fprintf(stderr, "[E::%s] fail to open file `%s'.\n", __func__, argv[2]);
exit(EXIT_FAILURE);
}
printf("before reading sequences\n");
bseq1_t *seqs = bseq_read_one_fasta_file(QUERY_DB_SIZE, &numReads, fp, &total_size);
if(seqs == NULL)
{
printf("ERROR! seqs = NULL\n");
exit(0);
}
int32_t *query_cum_len_ar = (int32_t *)_mm_malloc(numReads * sizeof(int32_t), 64);
FMI_search *fmiSearch = new FMI_search(argv[1]);
int readlength=atoi(argv[4]);
assert(readlength > 0);
assert(readlength < 10000);
assert(numReads > 0);
assert(numReads * readlength < QUERY_DB_SIZE);
uint8_t *enc_qdb=(uint8_t *)malloc(numReads*readlength*sizeof(uint8_t));
int64_t cind,st;
uint64_t r;
for (st=0; st < numReads; st++) {
query_cum_len_ar[st] = st * readlength;
cind=st*readlength;
for(r = 0; r < readlength; ++r) {
switch(seqs[st].seq[r])
{
case '0': enc_qdb[r+cind]=0;
break;
case '1': enc_qdb[r+cind]=1;
break;
case '2': enc_qdb[r+cind]=2;
break;
case '3': enc_qdb[r+cind]=3;
break;
default: enc_qdb[r+cind]=4;
}
//printf("%c %d\n", query_seq[r+cind], enc_qdb[r + cind]);
//printf("%d", enc_qdb[r + cind]);
}
}
int batch_size=0;
batch_size=atoi(argv[3]);
assert(batch_size > 0);
assert(batch_size <= numReads);
SMEM *matchArray = (SMEM *)_mm_malloc(numReads * readlength * sizeof(SMEM), 64);
int32_t minSeedLen = atoi(argv[5]);
int32_t max_mem_intv = atoi(argv[6]);
printf("minSeedLen = %d, max_mem_intv = %d\n", minSeedLen, max_mem_intv);
int numthreads=1;
int64_t numTotalSmem[numthreads];
#pragma omp parallel num_threads(numthreads)
{
int tid = omp_get_thread_num();
if(tid == 0)
printf("Running %d threads\n", omp_get_num_threads());
}
int32_t *max_intv_array = (int32_t *)_mm_malloc(numReads * sizeof(int32_t), 64);
int32_t i;
for(i = 0; i < numReads; i++)
{
max_intv_array[i] = max_mem_intv;
}
int64_t startTick, endTick;
#ifdef VTUNE_ANALYSIS
__itt_resume();
#endif
startTick = __rdtsc();
numthreads = 1;
numTotalSmem[0] = fmiSearch->bwtSeedStrategyAllPosOneThread(enc_qdb,
max_intv_array,
numReads,
seqs,
query_cum_len_ar,
minSeedLen,
matchArray);
endTick = __rdtsc();
#ifdef VTUNE_ANALYSIS
__itt_pause();
#endif
printf("Consumed: %ld cycles\n", endTick - startTick);
int64_t totalSmem = 0;
int tid;
for(tid = 0; tid < numthreads; tid++)
{
totalSmem += numTotalSmem[tid];
}
printf("totalSmems = %ld\n", totalSmem);
fmiSearch->sortSMEMs(matchArray,
numTotalSmem,
numReads,
readlength,
numthreads);
int32_t perThreadQuota = (numReads + (numthreads - 1)) / numthreads;
for(tid = 0; tid < numthreads; tid++)
{
int32_t first = tid * perThreadQuota;
SMEM *myMatchArray = matchArray + first * readlength;
int64_t i = 0;
int64_t rid;
for(rid = 0; rid < numReads; rid++)
{
while((i < numTotalSmem[tid]) && (myMatchArray[i].rid == rid))
{
SMEM smem = myMatchArray[i];
//printf("\n%u: ", smem.rid);
printf("[ %ld %ld %ld %u %u ] ", smem.k, smem.l, smem.s, smem.m, smem.n + 1);
i++;
}
printf("\n");
}
}
free(enc_qdb);
_mm_free(matchArray);
_mm_free(max_intv_array);
delete fmiSearch;
return 0;
}
|
