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#ifndef __BWA_UTILS_HPP__
#define __BWA_UTILS_HPP__
extern "C" {
#include "bwa.h"
#include "bwamem.h"
#include "kvec.h"
#include "utils.h"
}
namespace bwautils {
// Function modified from bwt_smem1a:
// https://github.com/lh3/bwa/blob/eb428d7d31ced059ad39af2701a22ebe6d175657/bwt.c#L289
/**
* Search for the k-mer of length @len starting at @q.
* Return true if an interval is found for the k-mer and false
* otherwise. The appropriate bwt interval will be placed
* in @resInterval upon success.
*
*/
bool getIntervalForKmer(const bwt_t* bwt, // the bwt index
int len, // k-mer length
const uint8_t *q, // query
bwtintv_t& resInterval);
// NOTE: $max_intv is not currently used in BWA-MEM
// NOTE: Modified from the original functions to take an initial interval for the search query
int bwt_smem1a_with_kmer(const bwt_t *bwt, int len, const uint8_t *q, int x, int min_intv, uint64_t max_intv, bwtintv_t initial_interval, bwtintv_v *mem, bwtintv_v *tmpvec[2]);
int bwt_smem1_with_kmer(const bwt_t *bwt, int len, const uint8_t *q, int x, int min_intv, bwtintv_t initial_interval, bwtintv_v *mem, bwtintv_v *tmpvec[2]);
}
#endif // __BWA_UTILS_HPP__
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