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NOT WORKING! find hom and het peaks

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This commit is contained in:
Heng Li
2020-03-24 18:50:52 -04:00
parent 2a848d254a
commit ec750cdd7d
1 changed files with 52 additions and 5 deletions
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yak-count.cpp
+52 -5
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@@ -378,22 +378,29 @@ static void yak_hist_line(int c, int x, int exceed, int64_t cnt)
fprintf(stderr, " %lld\n", (long long)cnt);
}
static int yak_analyze_count(int n_cnt, const int64_t *cnt)
int yak_analyze_count(int n_cnt, const int64_t *cnt, int *peak_het)
{
const int hist_max = 100;
int i, low_i, max_i;
int64_t max;
int i, low_i, max_i, max2_i, max3_i;
int64_t max, max2, max3, min;
// find the low point from the left
*peak_het = -1;
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
// find the highest peak
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]);
// print histogram
for (i = 2; i < n_cnt; ++i) {
int x, exceed = 0;
x = (int)((double)hist_max * cnt[i] / cnt[max_i] + .499);
@@ -409,12 +416,51 @@ static int yak_analyze_count(int n_cnt, const int64_t *cnt)
if (x > hist_max) exceed = 1, x = hist_max;
yak_hist_line(-1, x, exceed, rest);
}
return 0;
// look for smaller peak on the low end
max2 = -1; max2_i = -1;
for (i = max_i - 1; i > low_i; --i) {
if (cnt[i] >= cnt[i-1] && cnt[i] >= cnt[i+1]) {
if (cnt[i] > max2) max2 = cnt[i], max2_i = i;
}
}
if (max2_i > low_i && max2_i < max_i) {
for (i = max2_i + 1, min = max; i < max_i; ++i)
if (cnt[i] < min) min = cnt[i];
if (max2 < max * 0.05 || min > max2 * 0.95)
max2 = -1, max2_i = -1;
}
if (max2 > 0) fprintf(stderr, "[M::%s] left: count[%d] = %ld\n", __func__, max2_i, (long)cnt[max2_i]);
else fprintf(stderr, "[M::%s] left: none\n", __func__);
// look for smaller peak on the high end
max3 = -1; max3_i = -1;
for (i = max_i + 1; i < n_cnt - 1; ++i) {
if (cnt[i] >= cnt[i-1] && cnt[i] >= cnt[i+1]) {
if (cnt[i] > max3) max3 = cnt[i], max3_i = i;
}
}
if (max3_i > max_i) {
for (i = max_i + 1, min = max; i < max3_i; ++i)
if (cnt[i] < min) min = cnt[i];
if (max3 < max * 0.05 || min > max3 * 0.95 || max3_i > max_i * 2.5)
max3 = -1, max3_i = -1;
}
if (max3 > 0) fprintf(stderr, "[M::%s] right: count[%d] = %ld\n", __func__, max3_i, (long)cnt[max3_i]);
else fprintf(stderr, "[M::%s] right: none\n", __func__);
if (max3_i > 0) {
*peak_het = max_i;
return max3_i;
} else {
if (max2_i > 0) *peak_het = max2_i;
return max_i;
}
}
void ha_count_high(const hifiasm_opt_t *asm_opt)
{
int64_t cnt[YAK_N_COUNTS];
int peak_hom, peak_het;
yak_copt_t opt;
yak_ch_t *h;
yak_copt_init(&opt);
@@ -423,6 +469,7 @@ void ha_count_high(const hifiasm_opt_t *asm_opt)
opt.bf_shift = asm_opt->bf_shift;
h = yak_count_file(&opt, asm_opt->num_reads, asm_opt->read_file_names);
yak_ch_hist(h, cnt, opt.n_thread);
yak_analyze_count(YAK_N_COUNTS, cnt);
peak_hom = yak_analyze_count(YAK_N_COUNTS, cnt, &peak_het);
if (peak_hom > 0) fprintf(stderr, "[M::%s] peak_hom: %d; peak_het: %d\n", __func__, peak_hom, peak_het);
yak_ch_destroy(h);
}