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k-mer histogram

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This commit is contained in:
Heng Li
2020-03-24 16:02:23 -04:00
parent 64edb06e08
commit 2a848d254a
1 changed files with 48 additions and 3 deletions
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yak-count.cpp
+48 -3
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@@ -3,7 +3,7 @@
#include "yak.h" #include "yak.h"
#include "khashl.h" #include "khashl.h"
#define YAK_COUNTER_BITS 10 #define YAK_COUNTER_BITS 12
#define YAK_N_COUNTS (1<<YAK_COUNTER_BITS) #define YAK_N_COUNTS (1<<YAK_COUNTER_BITS)
#define YAK_MAX_COUNT ((1<<YAK_COUNTER_BITS)-1) #define YAK_MAX_COUNT ((1<<YAK_COUNTER_BITS)-1)
@@ -337,7 +337,7 @@ static void *worker_count_all(void *data, int step, void *in) // callback for kt
return 0; return 0;
} }
yak_ch_t *yak_count(const char *fn, const yak_copt_t *opt, yak_ch_t *h0) static yak_ch_t *yak_count(const char *fn, const yak_copt_t *opt, yak_ch_t *h0)
{ {
pldat_t pl; pldat_t pl;
gzFile fp; gzFile fp;
@@ -357,7 +357,7 @@ yak_ch_t *yak_count(const char *fn, const yak_copt_t *opt, yak_ch_t *h0)
return pl.h; return pl.h;
} }
yak_ch_t *yak_count_file(const yak_copt_t *opt, int n_fn, char **fn) static yak_ch_t *yak_count_file(const yak_copt_t *opt, int n_fn, char **fn)
{ {
int i; int i;
yak_ch_t *h = 0; yak_ch_t *h = 0;
@@ -368,6 +368,50 @@ yak_ch_t *yak_count_file(const yak_copt_t *opt, int n_fn, char **fn)
return h; return h;
} }
static void yak_hist_line(int c, int x, int exceed, int64_t cnt)
{
int j;
if (c >= 0) fprintf(stderr, "[M::%s] %5d: ", __func__, c);
else fprintf(stderr, "[M::%s] %5s: ", __func__, "rest");
for (j = 0; j < x; ++j) fputc('*', stderr);
if (exceed) fputc('>', stderr);
fprintf(stderr, " %lld\n", (long long)cnt);
}
static int yak_analyze_count(int n_cnt, const int64_t *cnt)
{
const int hist_max = 100;
int i, low_i, max_i;
int64_t max;
low_i = 2;
for (i = 3; i < n_cnt; ++i)
if (cnt[i] > cnt[i-1]) break;
low_i = i - 1;
fprintf(stderr, "[M::%s] lowest: count[%d] = %ld\n", __func__, low_i, (long)cnt[low_i]);
if (low_i == n_cnt - 1) return -1; // low coverage
max_i = low_i + 1, max = cnt[max_i];
for (i = low_i + 1; i < n_cnt; ++i)
if (cnt[i] > max)
max = cnt[i], max_i = i;
fprintf(stderr, "[M::%s] highest: count[%d] = %ld\n", __func__, max_i, (long)cnt[max_i]);
for (i = 2; i < n_cnt; ++i) {
int x, exceed = 0;
x = (int)((double)hist_max * cnt[i] / cnt[max_i] + .499);
if (x > hist_max) exceed = 1, x = hist_max; // may happen if cnt[2] is higher
if (i > max_i && x == 0) break;
yak_hist_line(i, x, exceed, cnt[i]);
}
{
int x, exceed = 0;
int64_t rest = 0;
for (; i < n_cnt; ++i) rest += cnt[i];
x = (int)((double)hist_max * rest / cnt[max_i] + .499);
if (x > hist_max) exceed = 1, x = hist_max;
yak_hist_line(-1, x, exceed, rest);
}
return 0;
}
void ha_count_high(const hifiasm_opt_t *asm_opt) void ha_count_high(const hifiasm_opt_t *asm_opt)
{ {
int64_t cnt[YAK_N_COUNTS]; int64_t cnt[YAK_N_COUNTS];
@@ -379,5 +423,6 @@ void ha_count_high(const hifiasm_opt_t *asm_opt)
opt.bf_shift = asm_opt->bf_shift; opt.bf_shift = asm_opt->bf_shift;
h = yak_count_file(&opt, asm_opt->num_reads, asm_opt->read_file_names); h = yak_count_file(&opt, asm_opt->num_reads, asm_opt->read_file_names);
yak_ch_hist(h, cnt, opt.n_thread); yak_ch_hist(h, cnt, opt.n_thread);
yak_analyze_count(YAK_N_COUNTS, cnt);
yak_ch_destroy(h); yak_ch_destroy(h);
} }