diff --git a/bwa.c b/bwa.c index 30e5284..80a4b8f 100644 --- a/bwa.c +++ b/bwa.c @@ -14,6 +14,7 @@ int bwa_verbose = 3; char bwa_rg_id[256]; +char *bwa_pg; /************************ * 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) 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); - err_printf("%s\n", bwa_pg); + if (bwa_pg) err_printf("%s\n", bwa_pg); } static char *bwa_escape(char *s) diff --git a/example.c b/example.c index a6c9bdd..96f25be 100644 --- a/example.c +++ b/example.c @@ -47,10 +47,10 @@ int main(int argc, char *argv[]) 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 // 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 - err_printf("%d%c", a.cigar[k]>>4, "MIDSH"[a.cigar[k]&0xf]); - err_printf("\t%d\n", a.NM); // print edit distance + printf("%d%c", a.cigar[k]>>4, "MIDSH"[a.cigar[k]&0xf]); + printf("\t%d\n", a.NM); // print edit distance free(a.cigar); // don't forget to deallocate CIGAR } free(ar.a); // and deallocate the hit list @@ -58,7 +58,7 @@ int main(int argc, char *argv[]) free(opt); kseq_destroy(ks); - err_gzclose(fp); + gzclose(fp); bwa_idx_destroy(idx); return 0; } diff --git a/main.c b/main.c index e0f0edb..1a18559 100644 --- a/main.c +++ b/main.c @@ -4,7 +4,7 @@ #include "utils.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.7.10-r912-dirty" +#define PACKAGE_VERSION "0.7.10-r915-dirty" #endif 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[]); -char *bwa_pg; - static int usage() { fprintf(stderr, "\n"); @@ -61,6 +59,7 @@ static int usage() int main(int argc, char *argv[]) { + extern char *bwa_pg; int i, ret; double t_real; kstring_t pg = {0,0,0};