62 lines
2.1 KiB
C
62 lines
2.1 KiB
C
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// To compile:
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// gcc -g -O2 example.c libminimap2.a -lz
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#include <stdlib.h>
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#include <assert.h>
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#include <stdio.h>
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#include <zlib.h>
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#include "minimap.h"
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#include "kseq.h"
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KSEQ_INIT(gzFile, gzread)
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int main(int argc, char *argv[])
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{
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mm_verbose = 2; // disable message output to stderr
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if (argc < 3) {
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fprintf(stderr, "Usage: minimap2-lite <target.fa> <query.fa>\n");
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return 1;
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}
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// open query file for reading; you may use your favorite FASTA/Q parser
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gzFile f = gzopen(argv[2], "r");
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assert(f);
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kseq_t *ks = kseq_init(f);
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// create index for target; we are creating one index for all target sequence
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int n_threads = 4, w = 10, k = 15, is_hpc = 0;
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mm_idx_t *mi = mm_idx_build(argv[1], w, k, is_hpc, n_threads);
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assert(mi);
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// mapping
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mm_mapopt_t opt;
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mm_mapopt_init(&opt); // initialize mapping parameters
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mm_mapopt_update(&opt, mi); // this sets the maximum minimizer occurrence; TODO: set a better default in mm_mapopt_init()!
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opt.flag |= MM_F_CIGAR; // perform alignment
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mm_tbuf_t *tbuf = mm_tbuf_init(); // thread buffer; for multi-threading, allocate one tbuf for each thread
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while (kseq_read(ks) >= 0) { // each kseq_read() call reads one query sequence
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const mm_reg1_t *reg;
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int j, i, n_reg;
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// get all hits for the query
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reg = mm_map(mi, ks->seq.l, ks->seq.s, &n_reg, tbuf, &opt, 0);
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// traverse hits and print them out
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for (j = 0; j < n_reg; ++j) {
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const mm_reg1_t *r = ®[j];
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assert(r->p); // with MM_F_CIGAR, this should not be NULL
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printf("%s\t%d\t%d\t%d\t%c\t", ks->name.s, ks->seq.l, r->qs, r->qe, "+-"[r->rev]);
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printf("%s\t%d\t%d\t%d\t%d\t%d\t%d\tcg:Z:", mi->seq[r->rid].name, mi->seq[r->rid].len, r->rs, r->re,
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r->p->blen - r->p->n_ambi - r->p->n_diff, r->p->blen, r->mapq);
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for (i = 0; i < r->p->n_cigar; ++i) // IMPORTANT: this gives the CIGAR in the aligned regions. NO soft/hard clippings!
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printf("%d%c", r->p->cigar[i]>>4, "MIDSHN"[r->p->cigar[i]&0xf]);
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putchar('\n');
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}
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}
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mm_tbuf_destroy(tbuf);
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// deallocate index and close the query file
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mm_idx_destroy(mi);
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kseq_destroy(ks);
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gzclose(f);
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return 0;
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}
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