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#include <stdio.h>
#include <unistd.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include <stdint.h>
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "bwtaln.h"
#include "bwtgap.h"
#include "utils.h"
#include "bwa.h"
#ifdef HAVE_PTHREAD
#include <pthread.h>
#endif
#ifdef USE_MALLOC_WRAPPERS
# include "malloc_wrap.h"
#endif
gap_opt_t *gap_init_opt()
{
gap_opt_t *o;
o = (gap_opt_t*)calloc(1, sizeof(gap_opt_t));
/* IMPORTANT: s_mm*10 should be about the average base error
rate. Voilating this requirement will break pairing! */
o->s_mm = 3; o->s_gapo = 11; o->s_gape = 4;
o->max_diff = -1; o->max_gapo = 1; o->max_gape = 6;
o->indel_end_skip = 5; o->max_del_occ = 10; o->max_entries = 2000000;
o->mode = BWA_MODE_GAPE | BWA_MODE_COMPREAD;
o->seed_len = 32; o->max_seed_diff = 2;
o->fnr = 0.04;
o->n_threads = 1;
o->max_top2 = 30;
o->trim_qual = 0;
return o;
}
int bwa_cal_maxdiff(int l, double err, double thres)
{
double elambda = exp(-l * err);
double sum, y = 1.0;
int k, x = 1;
for (k = 1, sum = elambda; k < 1000; ++k) {
y *= l * err;
x *= k;
sum += elambda * y / x;
if (1.0 - sum < thres) return k;
}
return 2;
}
// width must be filled as zero
int bwt_cal_width(const bwt_t *bwt, int len, const ubyte_t *str, bwt_width_t *width)
{
bwtint_t k, l, ok, ol;
int i, bid;
bid = 0;
k = 0; l = bwt->seq_len;
for (i = 0; i < len; ++i) {
ubyte_t c = str[i];
if (c < 4) {
bwt_2occ(bwt, k - 1, l, c, &ok, &ol);
k = bwt->L2[c] + ok + 1;
l = bwt->L2[c] + ol;
}
if (k > l || c > 3) { // then restart
k = 0;
l = bwt->seq_len;
++bid;
}
width[i].w = l - k + 1;
width[i].bid = bid;
}
width[len].w = 0;
width[len].bid = ++bid;
return bid;
}
void bwa_cal_sa_reg_gap(int tid, bwt_t *const bwt, int n_seqs, bwa_seq_t *seqs, const gap_opt_t *opt)
{
int i, j, max_l = 0, max_len;
gap_stack_t *stack;
bwt_width_t *w, *seed_w;
gap_opt_t local_opt = *opt;
// initiate priority stack
for (i = max_len = 0; i != n_seqs; ++i)
if (seqs[i].len > max_len) max_len = seqs[i].len;
if (opt->fnr > 0.0) local_opt.max_diff = bwa_cal_maxdiff(max_len, BWA_AVG_ERR, opt->fnr);
if (local_opt.max_diff < local_opt.max_gapo) local_opt.max_gapo = local_opt.max_diff;
stack = gap_init_stack(local_opt.max_diff, local_opt.max_gapo, local_opt.max_gape, &local_opt);
seed_w = (bwt_width_t*)calloc(opt->seed_len+1, sizeof(bwt_width_t));
w = 0;
for (i = 0; i != n_seqs; ++i) {
bwa_seq_t *p = seqs + i;
#ifdef HAVE_PTHREAD
if (i % opt->n_threads != tid) continue;
#endif
p->sa = 0; p->type = BWA_TYPE_NO_MATCH; p->c1 = p->c2 = 0; p->n_aln = 0; p->aln = 0;
if (max_l < p->len) {
max_l = p->len;
w = (bwt_width_t*)realloc(w, (max_l + 1) * sizeof(bwt_width_t));
memset(w, 0, (max_l + 1) * sizeof(bwt_width_t));
}
bwt_cal_width(bwt, p->len, p->seq, w);
if (opt->fnr > 0.0) local_opt.max_diff = bwa_cal_maxdiff(p->len, BWA_AVG_ERR, opt->fnr);
local_opt.seed_len = opt->seed_len < p->len? opt->seed_len : 0x7fffffff;
if (p->len > opt->seed_len)
bwt_cal_width(bwt, opt->seed_len, p->seq + (p->len - opt->seed_len), seed_w);
// core function
for (j = 0; j < p->len; ++j) // we need to complement
p->seq[j] = p->seq[j] > 3? 4 : 3 - p->seq[j];
p->aln = bwt_match_gap(bwt, p->len, p->seq, w, p->len <= opt->seed_len? 0 : seed_w, &local_opt, &p->n_aln, stack);
//fprintf(stderr, "mm=%lld,ins=%lld,del=%lld,gapo=%lld\n", p->aln->n_mm, p->aln->n_ins, p->aln->n_del, p->aln->n_gapo);
// clean up the unused data in the record
free(p->name); free(p->seq); free(p->rseq); free(p->qual);
p->name = 0; p->seq = p->rseq = p->qual = 0;
}
free(seed_w); free(w);
gap_destroy_stack(stack);
}
#ifdef HAVE_PTHREAD
typedef struct {
int tid;
bwt_t *bwt;
int n_seqs;
bwa_seq_t *seqs;
const gap_opt_t *opt;
} thread_aux_t;
static void *worker(void *data)
{
thread_aux_t *d = (thread_aux_t*)data;
bwa_cal_sa_reg_gap(d->tid, d->bwt, d->n_seqs, d->seqs, d->opt);
return 0;
}
#endif
bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa)
{
bwa_seqio_t *ks;
if (mode & BWA_MODE_BAM) { // open BAM
int which = 0;
if (mode & BWA_MODE_BAM_SE) which |= 4;
if (mode & BWA_MODE_BAM_READ1) which |= 1;
if (mode & BWA_MODE_BAM_READ2) which |= 2;
if (which == 0) which = 7; // then read all reads
ks = bwa_bam_open(fn_fa, which);
} else ks = bwa_seq_open(fn_fa);
return ks;
}
void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt)
{
int i, n_seqs, tot_seqs = 0;
bwa_seq_t *seqs;
bwa_seqio_t *ks;
clock_t t;
bwt_t *bwt;
// initialization
ks = bwa_open_reads(opt->mode, fn_fa);
{ // load BWT
char *str = (char*)calloc(strlen(prefix) + 10, 1);
strcpy(str, prefix); strcat(str, ".bwt"); bwt = bwt_restore_bwt(str);
free(str);
}
// core loop
err_fwrite(SAI_MAGIC, 1, 4, stdout);
err_fwrite(opt, sizeof(gap_opt_t), 1, stdout);
while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, opt->mode, opt->trim_qual)) != 0) {
tot_seqs += n_seqs;
t = clock();
fprintf(stderr, "[bwa_aln_core] calculate SA coordinate... ");
#ifdef HAVE_PTHREAD
if (opt->n_threads <= 1) { // no multi-threading at all
bwa_cal_sa_reg_gap(0, bwt, n_seqs, seqs, opt);
} else {
pthread_t *tid;
pthread_attr_t attr;
thread_aux_t *data;
int j;
pthread_attr_init(&attr);
pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
data = (thread_aux_t*)calloc(opt->n_threads, sizeof(thread_aux_t));
tid = (pthread_t*)calloc(opt->n_threads, sizeof(pthread_t));
for (j = 0; j < opt->n_threads; ++j) {
data[j].tid = j; data[j].bwt = bwt;
data[j].n_seqs = n_seqs; data[j].seqs = seqs; data[j].opt = opt;
pthread_create(&tid[j], &attr, worker, data + j);
}
for (j = 0; j < opt->n_threads; ++j) pthread_join(tid[j], 0);
free(data); free(tid);
}
#else
bwa_cal_sa_reg_gap(0, bwt, n_seqs, seqs, opt);
#endif
fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
t = clock();
fprintf(stderr, "[bwa_aln_core] write to the disk... ");
for (i = 0; i < n_seqs; ++i) {
bwa_seq_t *p = seqs + i;
err_fwrite(&p->n_aln, 4, 1, stdout);
if (p->n_aln) err_fwrite(p->aln, sizeof(bwt_aln1_t), p->n_aln, stdout);
}
fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
bwa_free_read_seq(n_seqs, seqs);
fprintf(stderr, "[bwa_aln_core] %d sequences have been processed.\n", tot_seqs);
}
// destroy
bwt_destroy(bwt);
bwa_seq_close(ks);
}
int bwa_aln(int argc, char *argv[])
{
int c, opte = -1;
gap_opt_t *opt;
char *prefix;
opt = gap_init_opt();
while ((c = getopt(argc, argv, "n:o:e:i:d:l:k:LR:m:t:NM:O:E:q:f:b012IYB:")) >= 0) {
switch (c) {
case 'n':
if (strstr(optarg, ".")) opt->fnr = atof(optarg), opt->max_diff = -1;
else opt->max_diff = atoi(optarg), opt->fnr = -1.0;
break;
case 'o': opt->max_gapo = atoi(optarg); break;
case 'e': opte = atoi(optarg); break;
case 'M': opt->s_mm = atoi(optarg); break;
case 'O': opt->s_gapo = atoi(optarg); break;
case 'E': opt->s_gape = atoi(optarg); break;
case 'd': opt->max_del_occ = atoi(optarg); break;
case 'i': opt->indel_end_skip = atoi(optarg); break;
case 'l': opt->seed_len = atoi(optarg); break;
case 'k': opt->max_seed_diff = atoi(optarg); break;
case 'm': opt->max_entries = atoi(optarg); break;
case 't': opt->n_threads = atoi(optarg); break;
case 'L': opt->mode |= BWA_MODE_LOGGAP; break;
case 'R': opt->max_top2 = atoi(optarg); break;
case 'q': opt->trim_qual = atoi(optarg); break;
case 'N': opt->mode |= BWA_MODE_NONSTOP; opt->max_top2 = 0x7fffffff; break;
case 'f': xreopen(optarg, "wb", stdout); break;
case 'b': opt->mode |= BWA_MODE_BAM; break;
case '0': opt->mode |= BWA_MODE_BAM_SE; break;
case '1': opt->mode |= BWA_MODE_BAM_READ1; break;
case '2': opt->mode |= BWA_MODE_BAM_READ2; break;
case 'I': opt->mode |= BWA_MODE_IL13; break;
case 'Y': opt->mode |= BWA_MODE_CFY; break;
case 'B': opt->mode |= atoi(optarg) << 24; break;
default: return 1;
}
}
if (opte > 0) {
opt->max_gape = opte;
opt->mode &= ~BWA_MODE_GAPE;
}
if (optind + 2 > argc) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: bwa aln [options] <prefix> <in.fq>\n\n");
fprintf(stderr, "Options: -n NUM max #diff (int) or missing prob under %.2f err rate (float) [%.2f]\n",
BWA_AVG_ERR, opt->fnr);
fprintf(stderr, " -o INT maximum number or fraction of gap opens [%d]\n", opt->max_gapo);
fprintf(stderr, " -e INT maximum number of gap extensions, -1 for disabling long gaps [-1]\n");
fprintf(stderr, " -i INT do not put an indel within INT bp towards the ends [%d]\n", opt->indel_end_skip);
fprintf(stderr, " -d INT maximum occurrences for extending a long deletion [%d]\n", opt->max_del_occ);
fprintf(stderr, " -l INT seed length [%d]\n", opt->seed_len);
fprintf(stderr, " -k INT maximum differences in the seed [%d]\n", opt->max_seed_diff);
fprintf(stderr, " -m INT maximum entries in the queue [%d]\n", opt->max_entries);
fprintf(stderr, " -t INT number of threads [%d]\n", opt->n_threads);
fprintf(stderr, " -M INT mismatch penalty [%d]\n", opt->s_mm);
fprintf(stderr, " -O INT gap open penalty [%d]\n", opt->s_gapo);
fprintf(stderr, " -E INT gap extension penalty [%d]\n", opt->s_gape);
fprintf(stderr, " -R INT stop searching when there are >INT equally best hits [%d]\n", opt->max_top2);
fprintf(stderr, " -q INT quality threshold for read trimming down to %dbp [%d]\n", BWA_MIN_RDLEN, opt->trim_qual);
fprintf(stderr, " -f FILE file to write output to instead of stdout\n");
fprintf(stderr, " -B INT length of barcode\n");
fprintf(stderr, " -L log-scaled gap penalty for long deletions\n");
fprintf(stderr, " -N non-iterative mode: search for all n-difference hits (slooow)\n");
fprintf(stderr, " -I the input is in the Illumina 1.3+ FASTQ-like format\n");
fprintf(stderr, " -b the input read file is in the BAM format\n");
fprintf(stderr, " -0 use single-end reads only (effective with -b)\n");
fprintf(stderr, " -1 use the 1st read in a pair (effective with -b)\n");
fprintf(stderr, " -2 use the 2nd read in a pair (effective with -b)\n");
fprintf(stderr, " -Y filter Casava-filtered sequences\n");
fprintf(stderr, "\n");
return 1;
}
if (opt->fnr > 0.0) {
int i, k;
for (i = 17, k = 0; i <= 250; ++i) {
int l = bwa_cal_maxdiff(i, BWA_AVG_ERR, opt->fnr);
if (l != k) fprintf(stderr, "[bwa_aln] %dbp reads: max_diff = %d\n", i, l);
k = l;
}
}
if ((prefix = bwa_idx_infer_prefix(argv[optind])) == 0) {
fprintf(stderr, "[%s] fail to locate the index\n", __func__);
free(opt);
return 1;
}
bwa_aln_core(prefix, argv[optind+1], opt);
free(opt); free(prefix);
return 0;
}
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