#include <string.h>
#include "bam.h"
#include "bam2bcf.h"
-#include "ksort.h"
#include "kaln.h"
#include "kprobaln.h"
#include "khash.h"
KHASH_SET_INIT_STR(rg)
+#include "ksort.h"
+KSORT_INIT_GENERIC(uint32_t)
+
#define MINUS_CONST 0x10000000
#define INDEL_WINDOW_SIZE 50
int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
const void *rghash)
{
- extern void ks_introsort_uint32_t(int, uint32_t*);
int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2;
int N, K, l_run, ref_type, n_alt;
char *inscns = 0, *ref2, *query, **ref_sample;