static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
+#define __g_skip_aln(b) (((b)->core.qual < g_min_mapQ) || ((b->core.flag & g_flag_on) != g_flag_on) \
+ || (b->core.flag & g_flag_off))
+
// callback function for bam_fetch()
static int view_func(const bam1_t *b, void *data)
{
- if (b->core.qual < g_min_mapQ) return 0;
- if (g_flag_on && (b->core.flag & g_flag_on) == 0) return 0;
- if (b->core.flag & g_flag_off) return 0;
- samwrite((samfile_t*)data, b);
+ if (!__g_skip_aln(b)) samwrite((samfile_t*)data, b);
return 0;
}
bam1_t *b = bam_init1();
int r;
while ((r = samread(in, b)) >= 0) // read one alignment from `in'
- samwrite(out, b); // write the alignment to `out'
+ if (!__g_skip_aln(b))
+ samwrite(out, b); // write the alignment to `out'
if (r < -1) fprintf(stderr, "[main_samview] truncated file.\n");
bam_destroy1(b);
} else { // retrieve alignments in specified regions