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r915: fixed broken example.c

This commit is contained in:
Heng Li 2014-10-17 16:17:28 -04:00
parent a55aac8a43
commit a06646493b
3 changed files with 8 additions and 8 deletions
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3
bwa.c
View File

@ -14,6 +14,7 @@
int bwa_verbose = 3; int bwa_verbose = 3;
char bwa_rg_id[256]; char bwa_rg_id[256];
char *bwa_pg;
/************************ /************************
* Batch FASTA/Q reader * * Batch FASTA/Q reader *
@ -352,7 +353,7 @@ void bwa_print_sam_hdr(const bntseq_t *bns, const char *rg_line)
for (i = 0; i < bns->n_seqs; ++i) for (i = 0; i < bns->n_seqs; ++i)
err_printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len); err_printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
if (rg_line) err_printf("%s\n", rg_line); if (rg_line) err_printf("%s\n", rg_line);
err_printf("%s\n", bwa_pg); if (bwa_pg) err_printf("%s\n", bwa_pg);
} }
static char *bwa_escape(char *s) static char *bwa_escape(char *s)

8
example.c
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@ -47,10 +47,10 @@ int main(int argc, char *argv[])
if (ar.a[i].secondary >= 0) continue; // skip secondary alignments if (ar.a[i].secondary >= 0) continue; // skip secondary alignments
a = mem_reg2aln(opt, idx->bns, idx->pac, ks->seq.l, ks->seq.s, &ar.a[i]); // get forward-strand position and CIGAR a = mem_reg2aln(opt, idx->bns, idx->pac, ks->seq.l, ks->seq.s, &ar.a[i]); // get forward-strand position and CIGAR
// print alignment // print alignment
err_printf("%s\t%c\t%s\t%ld\t%d\t", ks->name.s, "+-"[a.is_rev], idx->bns->anns[a.rid].name, (long)a.pos, a.mapq); printf("%s\t%c\t%s\t%ld\t%d\t", ks->name.s, "+-"[a.is_rev], idx->bns->anns[a.rid].name, (long)a.pos, a.mapq);
for (k = 0; k < a.n_cigar; ++k) // print CIGAR for (k = 0; k < a.n_cigar; ++k) // print CIGAR
err_printf("%d%c", a.cigar[k]>>4, "MIDSH"[a.cigar[k]&0xf]); printf("%d%c", a.cigar[k]>>4, "MIDSH"[a.cigar[k]&0xf]);
err_printf("\t%d\n", a.NM); // print edit distance printf("\t%d\n", a.NM); // print edit distance
free(a.cigar); // don't forget to deallocate CIGAR free(a.cigar); // don't forget to deallocate CIGAR
} }
free(ar.a); // and deallocate the hit list free(ar.a); // and deallocate the hit list
@ -58,7 +58,7 @@ int main(int argc, char *argv[])
free(opt); free(opt);
kseq_destroy(ks); kseq_destroy(ks);
err_gzclose(fp); gzclose(fp);
bwa_idx_destroy(idx); bwa_idx_destroy(idx);
return 0; return 0;
} }

5
main.c
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@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.10-r912-dirty" #define PACKAGE_VERSION "0.7.10-r915-dirty"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);
@ -26,8 +26,6 @@ int main_shm(int argc, char *argv[]);
int main_pemerge(int argc, char *argv[]); int main_pemerge(int argc, char *argv[]);
char *bwa_pg;
static int usage() static int usage()
{ {
fprintf(stderr, "\n"); fprintf(stderr, "\n");
@ -61,6 +59,7 @@ static int usage()
int main(int argc, char *argv[]) int main(int argc, char *argv[])
{ {
extern char *bwa_pg;
int i, ret; int i, ret;
double t_real; double t_real;
kstring_t pg = {0,0,0}; kstring_t pg = {0,0,0};