fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
} else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
}
fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
} else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
}
} else if (mode[0] == 'w') { // write
fp->header = bam_header_dup((const bam_header_t*)aux);
if (mode[1] == 'b') { // binary
} else if (mode[0] == 'w') { // write
fp->header = bam_header_dup((const bam_header_t*)aux);
if (mode[1] == 'b') { // binary
- fp->x.bam = strcmp(fn, "-")? bam_open(fn, "w") : bam_dopen(fileno(stdout), "w");
+ fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode);
if (fp->x.bam == 0) goto open_err_ret;
bam_header_write(fp->x.bam, fp->header);
} else { // text
if (fp->x.bam == 0) goto open_err_ret;
bam_header_write(fp->x.bam, fp->header);
} else { // text
-int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
+int sampileup(samfile_t *fp, int mask, int min_mapQ, bam_pileup_f func, void *func_data)
buf = bam_plbuf_init(func, func_data);
bam_plbuf_set_mask(buf, mask);
while ((ret = samread(fp, b)) >= 0)
buf = bam_plbuf_init(func, func_data);
bam_plbuf_set_mask(buf, mask);
while ((ret = samread(fp, b)) >= 0)