#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
+#include <assert.h>
#include "sam.h"
typedef struct __linkbuf_t {
int ret = 1, is_restart = 1;
if (c->flag&BAM_FUNMAP) return 0; // unmapped read
- assert(x <= pos);
+ assert(x <= pos); // otherwise a bug
p->qpos = -1; p->indel = 0; p->is_del = p->is_head = p->is_tail = 0;
for (k = 0; k < c->n_cigar; ++k) {
int op = bam1_cigar(b)[k] & BAM_CIGAR_MASK; // operation
break;
}
}
- assert(x > pos);
+ assert(x > pos); // otherwise a bug
return ret;
}
buf->func(buf->tid, buf->pos, n_pu, buf->pu, buf->func_data);
}
// update tid and pos
- if (buf->head->next) assert(buf->tid <= buf->head->b.core.tid); // otherwise, not sorted
+ if (buf->head->next) {
+ if (buf->tid > buf->head->b.core.tid) {
+ fprintf(stderr, "[bam_plbuf_push] unsorted input. Pileup aborts.\n");
+ return 1;
+ }
+ }
if (buf->tid < buf->head->b.core.tid) { // come to a new reference sequence
buf->tid = buf->head->b.core.tid; buf->pos = buf->head->beg; // jump to the next reference
} else if (buf->pos < buf->head->beg) { // here: tid == head->b.core.tid