Is there a fastest way to ouput the unique kmer sequence ? not only output the kmer count

[xiongxu]

let kh_val(h)=y when put the key into hash?

[slw287r]

Not sure if this is efficient enough, you can unpack the kmer out of uint64_t given k to a seq string:

#include <inttypes.h>

void u64s(uint64_t x, char* s, size_t k)
{
	size_t i = 0;
	for (i = 0; i < k; ++i) {
		s[k - i - 1] = "ACGT"[(uint8_t) x & 0x3];
		x >>= 2;
	}
	s[i] = '\0';
}

static void print_hist(const kc_c1_t *h)
{
	int i, j = 31;
	khint_t k;
	uint64_t cnt[256] = {0};
	char s[j + 1];
	//for (i = 0; i < 256; ++i) cnt[i] = 0;
	for (k = 0; k < kh_end(h); ++k)
	{
		if (kh_exist(h, k))
		{
			u64s(kh_key(h, k), s, j);
			printf("%"PRIu64"\t%d\t%s\n", kh_key(h, k), kh_val(h, k), s);
			//++cnt[kh_val(h, k) < 256? kh_val(h, k) : 255];
		}
	}
	/*
	for (i = 1; i < 256; ++i)
		printf("%d\t%ld\n", i, (long)cnt[i]);
	*/
}

reference