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#include <zlib.h>
#include <stdio.h>
#include <unistd.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <math.h>
#include "bwa.h"
#include "bwamem.h"
#include "kvec.h"
#include "utils.h"
#include "kseq.h"
#include "utils.h"
KSEQ_DECLARE(gzFile)
extern unsigned char nst_nt4_table[256];
void *kopen(const char *fn, int *_fd);
int kclose(void *a);
static void update_a(mem_opt_t *opt, const mem_opt_t *opt0)
{
if (opt0->a) { // matching score is changed
if (!opt0->b) opt->b *= opt->a;
if (!opt0->T) opt->T *= opt->a;
if (!opt0->o_del) opt->o_del *= opt->a;
if (!opt0->e_del) opt->e_del *= opt->a;
if (!opt0->o_ins) opt->o_ins *= opt->a;
if (!opt0->e_ins) opt->e_ins *= opt->a;
if (!opt0->zdrop) opt->zdrop *= opt->a;
if (!opt0->pen_clip5) opt->pen_clip5 *= opt->a;
if (!opt0->pen_clip3) opt->pen_clip3 *= opt->a;
if (!opt0->pen_unpaired) opt->pen_unpaired *= opt->a;
}
}
int main_mem(int argc, char *argv[])
{
mem_opt_t *opt, opt0;
int fd, fd2, i, c, n, copy_comment = 0;
gzFile fp, fp2 = 0;
kseq_t *ks, *ks2 = 0;
bseq1_t *seqs;
bwaidx_t *idx;
char *p, *rg_line = 0;
const char *mode = 0;
void *ko = 0, *ko2 = 0;
int64_t n_processed = 0;
mem_pestat_t pes[4], *pes0 = 0;
memset(pes, 0, 4 * sizeof(mem_pestat_t));
for (i = 0; i < 4; ++i) pes[i].failed = 1;
opt = mem_opt_init();
memset(&opt0, 0, sizeof(mem_opt_t));
while ((c = getopt(argc, argv, "epaFMCSPHYk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:")) >= 0) {
if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
else if (c == 'x') mode = optarg;
else if (c == 'w') opt->w = atoi(optarg), opt0.w = 1;
else if (c == 'A') opt->a = atoi(optarg), opt0.a = 1;
else if (c == 'B') opt->b = atoi(optarg), opt0.b = 1;
else if (c == 'T') opt->T = atoi(optarg), opt0.T = 1;
else if (c == 'U') opt->pen_unpaired = atoi(optarg), opt0.pen_unpaired = 1;
else if (c == 't') opt->n_threads = atoi(optarg), opt->n_threads = opt->n_threads > 1? opt->n_threads : 1;
else if (c == 'P') opt->flag |= MEM_F_NOPAIRING;
else if (c == 'a') opt->flag |= MEM_F_ALL;
else if (c == 'p') opt->flag |= MEM_F_PE;
else if (c == 'M') opt->flag |= MEM_F_NO_MULTI;
else if (c == 'S') opt->flag |= MEM_F_NO_RESCUE;
else if (c == 'e') opt->flag |= MEM_F_SELF_OVLP;
else if (c == 'F') opt->flag |= MEM_F_ALN_REG;
else if (c == 'Y') opt->flag |= MEM_F_SOFTCLIP;
else if (c == 'c') opt->max_occ = atoi(optarg), opt0.max_occ = 1;
else if (c == 'd') opt->zdrop = atoi(optarg), opt0.zdrop = 1;
else if (c == 'v') bwa_verbose = atoi(optarg);
else if (c == 'r') opt->split_factor = atof(optarg), opt0.split_factor = 1.;
else if (c == 'D') opt->drop_ratio = atof(optarg), opt0.drop_ratio = 1.;
else if (c == 'm') opt->max_matesw = atoi(optarg), opt0.max_matesw = 1;
else if (c == 'h') opt->max_hits = atoi(optarg), opt0.max_hits = 1;
else if (c == 's') opt->split_width = atoi(optarg), opt0.split_width = 1;
else if (c == 'G') opt->max_chain_gap = atoi(optarg), opt0.max_chain_gap = 1;
else if (c == 'N') opt->max_chain_extend = atoi(optarg), opt0.max_chain_extend = 1;
else if (c == 'W') opt->min_chain_weight = atoi(optarg), opt0.min_chain_weight = 1;
else if (c == 'C') copy_comment = 1;
else if (c == 'Q') {
opt0.mapQ_coef_len = 1;
opt->mapQ_coef_len = atoi(optarg);
opt->mapQ_coef_fac = opt->mapQ_coef_len > 0? log(opt->mapQ_coef_len) : 0;
} else if (c == 'O') {
opt0.o_del = opt0.o_ins = 1;
opt->o_del = opt->o_ins = strtol(optarg, &p, 10);
if (*p != 0 && ispunct(*p) && isdigit(p[1]))
opt->o_ins = strtol(p+1, &p, 10);
} else if (c == 'E') {
opt0.e_del = opt0.e_ins = 1;
opt->e_del = opt->e_ins = strtol(optarg, &p, 10);
if (*p != 0 && ispunct(*p) && isdigit(p[1]))
opt->e_ins = strtol(p+1, &p, 10);
} else if (c == 'L') {
opt0.pen_clip5 = opt0.pen_clip3 = 1;
opt->pen_clip5 = opt->pen_clip3 = strtol(optarg, &p, 10);
if (*p != 0 && ispunct(*p) && isdigit(p[1]))
opt->pen_clip3 = strtol(p+1, &p, 10);
} else if (c == 'R') {
if ((rg_line = bwa_set_rg(optarg)) == 0) return 1; // FIXME: memory leak
} else if (c == 'I') { // specify the insert size distribution
pes0 = pes;
pes[1].failed = 0;
pes[1].avg = strtod(optarg, &p);
pes[1].std = pes[1].avg * .1;
if (*p != 0 && ispunct(*p) && isdigit(p[1]))
pes[1].std = strtod(p+1, &p);
pes[1].high = (int)(pes[1].avg + 4. * pes[1].std + .499);
pes[1].low = (int)(pes[1].avg - 4. * pes[1].std + .499);
if (pes[1].low < 1) pes[1].low = 1;
if (*p != 0 && ispunct(*p) && isdigit(p[1]))
pes[1].high = (int)(strtod(p+1, &p) + .499);
if (*p != 0 && ispunct(*p) && isdigit(p[1]))
pes[1].low = (int)(strtod(p+1, &p) + .499);
if (bwa_verbose >= 3)
fprintf(stderr, "[M::%s] mean insert size: %.3f, stddev: %.3f, max: %d, min: %d\n",
__func__, pes[1].avg, pes[1].std, pes[1].high, pes[1].low);
}
else return 1;
}
if (opt->n_threads < 1) opt->n_threads = 1;
if (optind + 1 >= argc || optind + 3 < argc) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: bwa mem [options] <idxbase> <in1.fq> [in2.fq]\n\n");
fprintf(stderr, "Algorithm options:\n\n");
fprintf(stderr, " -t INT number of threads [%d]\n", opt->n_threads);
fprintf(stderr, " -k INT minimum seed length [%d]\n", opt->min_seed_len);
fprintf(stderr, " -w INT band width for banded alignment [%d]\n", opt->w);
fprintf(stderr, " -d INT off-diagonal X-dropoff [%d]\n", opt->zdrop);
fprintf(stderr, " -r FLOAT look for internal seeds inside a seed longer than {-k} * FLOAT [%g]\n", opt->split_factor);
// fprintf(stderr, " -s INT look for internal seeds inside a seed with less than INT occ [%d]\n", opt->split_width);
fprintf(stderr, " -c INT skip seeds with more than INT occurrences [%d]\n", opt->max_occ);
fprintf(stderr, " -D FLOAT drop chains shorter than FLOAT fraction of the longest overlapping chain [%.2f]\n", opt->drop_ratio);
fprintf(stderr, " -W INT discard a chain if seeded bases shorter than INT [0]\n");
fprintf(stderr, " -m INT perform at most INT rounds of mate rescues for each read [%d]\n", opt->max_matesw);
fprintf(stderr, " -S skip mate rescue\n");
fprintf(stderr, " -P skip pairing; mate rescue performed unless -S also in use\n");
fprintf(stderr, " -e discard full-length exact matches\n");
fprintf(stderr, " -A INT score for a sequence match, which scales options -TdBOELU unless overridden [%d]\n", opt->a);
fprintf(stderr, " -B INT penalty for a mismatch [%d]\n", opt->b);
fprintf(stderr, " -O INT[,INT] gap open penalties for deletions and insertions [%d,%d]\n", opt->o_del, opt->o_ins);
fprintf(stderr, " -E INT[,INT] gap extension penalty; a gap of size k cost '{-O} + {-E}*k' [%d,%d]\n", opt->e_del, opt->e_ins);
fprintf(stderr, " -L INT[,INT] penalty for 5'- and 3'-end clipping [%d,%d]\n", opt->pen_clip5, opt->pen_clip3);
fprintf(stderr, " -U INT penalty for an unpaired read pair [%d]\n", opt->pen_unpaired);
fprintf(stderr, " -x STR read type. Setting -x changes multiple parameters unless overriden [null]\n");
fprintf(stderr, " pacbio: -k17 -W40 -r10 -A2 -B5 -O2 -E1 -L0\n");
fprintf(stderr, " pbread: -k13 -W40 -c1000 -r10 -A2 -B5 -O2 -E1 -N25 -FeaD.001\n");
fprintf(stderr, "\nInput/output options:\n\n");
fprintf(stderr, " -p first query file consists of interleaved paired-end sequences\n");
fprintf(stderr, " -R STR read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n");
fprintf(stderr, "\n");
fprintf(stderr, " -v INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging [%d]\n", bwa_verbose);
fprintf(stderr, " -T INT minimum score to output [%d]\n", opt->T);
fprintf(stderr, " -h INT if there are <INT hits with score >80%% of the max score, output all in XA [%d]\n", opt->max_hits);
fprintf(stderr, " -a output all alignments for SE or unpaired PE\n");
fprintf(stderr, " -C append FASTA/FASTQ comment to SAM output\n");
fprintf(stderr, " -Y use soft clipping for supplementary alignments\n");
fprintf(stderr, " -M mark shorter split hits as secondary\n\n");
fprintf(stderr, " -I FLOAT[,FLOAT[,INT[,INT]]]\n");
fprintf(stderr, " specify the mean, standard deviation (10%% of the mean if absent), max\n");
fprintf(stderr, " (4 sigma from the mean if absent) and min of the insert size distribution.\n");
fprintf(stderr, " FR orientation only. [inferred]\n");
fprintf(stderr, "\n");
fprintf(stderr, "Note: Please read the man page for detailed description of the command line and options.\n");
fprintf(stderr, "\n");
free(opt);
return 1;
}
if (mode) {
if (strcmp(mode, "pacbio") == 0 || strcmp(mode, "pbref") == 0 || strcmp(mode, "pbread1") == 0 || strcmp(mode, "pbread") == 0) {
if (!opt0.a) opt->a = 2, opt0.a = 1;
update_a(opt, &opt0);
if (!opt0.o_del) opt->o_del = 2;
if (!opt0.e_del) opt->e_del = 1;
if (!opt0.o_ins) opt->o_ins = 2;
if (!opt0.e_ins) opt->e_ins = 1;
if (!opt0.b) opt->b = 5;
if (opt0.split_factor == 0.) opt->split_factor = 10.;
if (!opt0.min_chain_weight) opt->min_chain_weight = 40;
if (strcmp(mode, "pbread1") == 0 || strcmp(mode, "pbread") == 0) {
opt->flag |= MEM_F_ALL | MEM_F_SELF_OVLP | MEM_F_ALN_REG;
if (!opt0.max_occ) opt->max_occ = 1000;
if (!opt0.min_seed_len) opt->min_seed_len = 13;
if (!opt0.max_chain_extend) opt->max_chain_extend = 25;
if (opt0.drop_ratio == 0.) opt->drop_ratio = .001;
} else {
if (!opt0.min_seed_len) opt->min_seed_len = 17;
if (!opt0.pen_clip5) opt->pen_clip5 = 0;
if (!opt0.pen_clip3) opt->pen_clip3 = 0;
}
} else {
fprintf(stderr, "[E::%s] unknown read type '%s'\n", __func__, mode);
return 1; // FIXME memory leak
}
} else update_a(opt, &opt0);
// if (opt->T < opt->min_HSP_score) opt->T = opt->min_HSP_score; // TODO: tie ->T to MEM_HSP_COEF
bwa_fill_scmat(opt->a, opt->b, opt->mat);
if ((idx = bwa_idx_load(argv[optind], BWA_IDX_ALL)) == 0) return 1; // FIXME: memory leak
ko = kopen(argv[optind + 1], &fd);
if (ko == 0) {
if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] fail to open file `%s'.\n", __func__, argv[optind + 1]);
return 1;
}
fp = gzdopen(fd, "r");
ks = kseq_init(fp);
if (optind + 2 < argc) {
if (opt->flag&MEM_F_PE) {
if (bwa_verbose >= 2)
fprintf(stderr, "[W::%s] when '-p' is in use, the second query file will be ignored.\n", __func__);
} else {
ko2 = kopen(argv[optind + 2], &fd2);
if (ko2 == 0) {
if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] fail to open file `%s'.\n", __func__, argv[optind + 2]);
return 1;
}
fp2 = gzdopen(fd2, "r");
ks2 = kseq_init(fp2);
opt->flag |= MEM_F_PE;
}
}
if (!(opt->flag & MEM_F_ALN_REG))
bwa_print_sam_hdr(idx->bns, rg_line);
while ((seqs = bseq_read(opt->chunk_size * opt->n_threads, &n, ks, ks2)) != 0) {
int64_t size = 0;
if ((opt->flag & MEM_F_PE) && (n&1) == 1) {
if (bwa_verbose >= 2)
fprintf(stderr, "[W::%s] odd number of reads in the PE mode; last read dropped\n", __func__);
n = n>>1<<1;
}
if (!copy_comment)
for (i = 0; i < n; ++i) {
free(seqs[i].comment); seqs[i].comment = 0;
}
for (i = 0; i < n; ++i) size += seqs[i].l_seq;
if (bwa_verbose >= 3)
fprintf(stderr, "[M::%s] read %d sequences (%ld bp)...\n", __func__, n, (long)size);
mem_process_seqs(opt, idx->bwt, idx->bns, idx->pac, n_processed, n, seqs, pes0);
n_processed += n;
for (i = 0; i < n; ++i) {
if (seqs[i].sam) err_fputs(seqs[i].sam, stdout);
free(seqs[i].name); free(seqs[i].comment); free(seqs[i].seq); free(seqs[i].qual); free(seqs[i].sam);
}
free(seqs);
}
free(opt);
bwa_idx_destroy(idx);
kseq_destroy(ks);
err_gzclose(fp); kclose(ko);
if (ks2) {
kseq_destroy(ks2);
err_gzclose(fp2); kclose(ko2);
}
return 0;
}
int main_fastmap(int argc, char *argv[])
{
int c, i, min_iwidth = 20, min_len = 17, print_seq = 0;
kseq_t *seq;
bwtint_t k;
gzFile fp;
smem_i *itr;
const bwtintv_v *a;
bwaidx_t *idx;
while ((c = getopt(argc, argv, "w:l:p")) >= 0) {
switch (c) {
case 'p': print_seq = 1; break;
case 'w': min_iwidth = atoi(optarg); break;
case 'l': min_len = atoi(optarg); break;
default: return 1;
}
}
if (optind + 1 >= argc) {
fprintf(stderr, "Usage: bwa fastmap [-p] [-l minLen=%d] [-w maxSaSize=%d] <idxbase> <in.fq>\n", min_len, min_iwidth);
return 1;
}
fp = xzopen(argv[optind + 1], "r");
seq = kseq_init(fp);
if ((idx = bwa_idx_load(argv[optind], BWA_IDX_BWT|BWA_IDX_BNS)) == 0) return 1;
itr = smem_itr_init(idx->bwt);
while (kseq_read(seq) >= 0) {
err_printf("SQ\t%s\t%ld", seq->name.s, seq->seq.l);
if (print_seq) {
err_putchar('\t');
err_puts(seq->seq.s);
} else err_putchar('\n');
for (i = 0; i < seq->seq.l; ++i)
seq->seq.s[i] = nst_nt4_table[(int)seq->seq.s[i]];
smem_set_query(itr, seq->seq.l, (uint8_t*)seq->seq.s);
while ((a = smem_next(itr)) != 0) {
for (i = 0; i < a->n; ++i) {
bwtintv_t *p = &a->a[i];
if ((uint32_t)p->info - (p->info>>32) < min_len) continue;
err_printf("EM\t%d\t%d\t%ld", (uint32_t)(p->info>>32), (uint32_t)p->info, (long)p->x[2]);
if (p->x[2] <= min_iwidth) {
for (k = 0; k < p->x[2]; ++k) {
bwtint_t pos;
int len, is_rev, ref_id;
len = (uint32_t)p->info - (p->info>>32);
pos = bns_depos(idx->bns, bwt_sa(idx->bwt, p->x[0] + k), &is_rev);
if (is_rev) pos -= len - 1;
bns_cnt_ambi(idx->bns, pos, len, &ref_id);
err_printf("\t%s:%c%ld", idx->bns->anns[ref_id].name, "+-"[is_rev], (long)(pos - idx->bns->anns[ref_id].offset) + 1);
}
} else err_puts("\t*");
err_putchar('\n');
}
}
err_puts("//");
}
smem_itr_destroy(itr);
bwa_idx_destroy(idx);
kseq_destroy(seq);
err_gzclose(fp);
return 0;
}
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