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r369: updated example with the latest API

This commit is contained in:
Heng Li 2017-09-14 22:44:10 -04:00
parent 75ff7ceec5
commit 14b853499f
2 changed files with 36 additions and 38 deletions
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67
example.c
View File

@ -11,53 +11,52 @@ KSEQ_INIT(gzFile, gzread)
int main(int argc, char *argv[])
{
mm_idxopt_t iopt;
mm_mapopt_t mopt;
int n_threads = 3;
mm_verbose = 2; // disable message output to stderr
mm_set_opt(0, &iopt, &mopt);
mopt.flag |= MM_F_CIGAR; // perform alignment
if (argc < 3) {
fprintf(stderr, "Usage: minimap2-lite <target.fa> <query.fa>\n");
return 1;
}
// open query file for reading; you may use your favorite FASTA/Q parser
gzFile f = gzopen(argv[2], "r");
assert(f);
kseq_t *ks = kseq_init(f);
// create index for target; we are creating one index for all target sequence
int n_threads = 4, w = 10, k = 15, is_hpc = 0;
mm_idx_t *mi = mm_idx_build(argv[1], w, k, is_hpc, n_threads);
assert(mi);
// mapping
mm_mapopt_t opt;
mm_mapopt_init(&opt); // initialize mapping parameters
mm_mapopt_update(&opt, mi); // this sets the maximum minimizer occurrence; TODO: set a better default in mm_mapopt_init()!
opt.flag |= MM_F_CIGAR; // perform alignment
mm_tbuf_t *tbuf = mm_tbuf_init(); // thread buffer; for multi-threading, allocate one tbuf for each thread
while (kseq_read(ks) >= 0) { // each kseq_read() call reads one query sequence
mm_reg1_t *reg;
int j, i, n_reg;
// get all hits for the query
reg = mm_map(mi, ks->seq.l, ks->seq.s, &n_reg, tbuf, &opt, 0);
// traverse hits and print them out
for (j = 0; j < n_reg; ++j) {
mm_reg1_t *r = &reg[j];
assert(r->p); // with MM_F_CIGAR, this should not be NULL
printf("%s\t%d\t%d\t%d\t%c\t", ks->name.s, ks->seq.l, r->qs, r->qe, "+-"[r->rev]);
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,
r->p->blen - r->p->n_ambi - r->p->n_diff, r->p->blen, r->mapq);
for (i = 0; i < r->p->n_cigar; ++i) // IMPORTANT: this gives the CIGAR in the aligned regions. NO soft/hard clippings!
printf("%d%c", r->p->cigar[i]>>4, "MIDSHN"[r->p->cigar[i]&0xf]);
putchar('\n');
free(r->p);
// open index reader
mm_idx_reader_t *r = mm_idx_reader_open(argv[1], &iopt, 0);
mm_idx_t *mi;
while ((mi = mm_idx_reader_read(r, n_threads)) != 0) { // traverse each part of the index
mm_mapopt_update(&mopt, mi); // this sets the maximum minimizer occurrence; TODO: set a better default in mm_mapopt_init()!
mm_tbuf_t *tbuf = mm_tbuf_init(); // thread buffer; for multi-threading, allocate one tbuf for each thread
while (kseq_read(ks) >= 0) { // each kseq_read() call reads one query sequence
mm_reg1_t *reg;
int j, i, n_reg;
reg = mm_map(mi, ks->seq.l, ks->seq.s, &n_reg, tbuf, &mopt, 0); // get all hits for the query
for (j = 0; j < n_reg; ++j) { // traverse hits and print them out
mm_reg1_t *r = &reg[j];
assert(r->p); // with MM_F_CIGAR, this should not be NULL
printf("%s\t%d\t%d\t%d\t%c\t", ks->name.s, ks->seq.l, r->qs, r->qe, "+-"[r->rev]);
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,
r->p->blen - r->p->n_ambi - r->p->n_diff, r->p->blen, r->mapq);
for (i = 0; i < r->p->n_cigar; ++i) // IMPORTANT: this gives the CIGAR in the aligned regions. NO soft/hard clippings!
printf("%d%c", r->p->cigar[i]>>4, "MIDSHN"[r->p->cigar[i]&0xf]);
putchar('\n');
free(r->p);
}
free(reg);
}
free(reg);
mm_tbuf_destroy(tbuf);
mm_idx_destroy(mi);
}
mm_tbuf_destroy(tbuf);
// deallocate index and close the query file
mm_idx_destroy(mi);
kseq_destroy(ks);
mm_idx_reader_close(r); // close the index reader
kseq_destroy(ks); // close the query file
gzclose(f);
return 0;
}

7
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.1.1-r368-dirty"
#define MM_VERSION "2.1.1-r369-dirty"
#ifdef __linux__
#include <sys/resource.h>
@ -67,6 +67,7 @@ int main(int argc, char *argv[])
char *fnw = 0, *rg = 0, *s;
FILE *fp_help = stderr;
mm_idx_reader_t *idx_rdr;
mm_idx_t *mi;
liftrlimit();
mm_realtime0 = realtime();
@ -210,9 +211,7 @@ int main(int argc, char *argv[])
}
if (opt.flag & MM_F_OUT_SAM)
mm_write_sam_hdr_no_SQ(rg, MM_VERSION, argc, argv);
for (;;) {
mm_idx_t *mi;
if ((mi = mm_idx_reader_read(idx_rdr, n_threads)) == 0) break;
while ((mi = mm_idx_reader_read(idx_rdr, n_threads)) != 0) {
if (mm_verbose >= 2 && idx_rdr->n_parts > 1 && (opt.flag&MM_F_OUT_SAM) && !(opt.flag&MM_F_NO_SAM_SQ))
fprintf(stderr, "[WARNING] \033[1;31mSAM output is malformated due to internal @SQ lines. Please add option --no-sam-sq or filter afterwards.\033[0m\n");
if (mm_verbose >= 3)