typedef struct {
int i;
- uint64_t pos;
+ uint64_t pos, idx;
bam1_t *b;
} heap1_t;
+#define __pos_cmp(a, b) ((a).pos > (b).pos || ((a).pos == (b).pos && ((a).i > (b).i || ((a).i == (b).i && (a).idx > (b).idx))))
+
static inline int heap_lt(const heap1_t a, const heap1_t b)
{
if (g_is_by_qname) {
int t;
if (a.b == 0 || b.b == 0) return a.b == 0? 1 : 0;
t = strnum_cmp(bam1_qname(a.b), bam1_qname(b.b));
- return (t > 0 || (t == 0 && a.pos > b.pos));
- } else return (a.pos > b.pos);
+ return (t > 0 || (t == 0 && __pos_cmp(a, b)));
+ } else return __pos_cmp(a, b);
}
KSORT_INIT(heap, heap1_t, heap_lt)
bam_header_t *hout = 0;
bam_header_t *hheaders = NULL;
int i, j;
+ uint64_t idx = 0;
if (headers) {
tamFile fpheaders = sam_open(headers);
h = heap + i;
h->i = i;
h->b = (bam1_t*)calloc(1, sizeof(bam1_t));
- if (bam_read1(fp[i], h->b) >= 0)
+ if (bam_read1(fp[i], h->b) >= 0) {
h->pos = ((uint64_t)h->b->core.tid<<32) | (uint32_t)h->b->core.pos<<1 | bam1_strand(h->b);
+ h->idx = idx++;
+ }
else h->pos = HEAP_EMPTY;
}
fpout = strcmp(out, "-")? bam_open(out, "w") : bam_dopen(fileno(stdout), "w");
bam_write1_core(fpout, &b->core, b->data_len, b->data);
if ((j = bam_read1(fp[heap->i], b)) >= 0) {
heap->pos = ((uint64_t)b->core.tid<<32) | (uint32_t)b->core.pos<<1 | bam1_strand(b);
+ heap->idx = idx++;
} else if (j == -1) {
heap->pos = HEAP_EMPTY;
free(heap->b->data); free(heap->b);