void get_windowed_ins_probs2(int win_length)
{
// Allocate two arrays for ins. prob over each window of length win_length over each sequence.
double* winned_ins_probs1 = (double*)malloc(sizeof(double) * global_aln_info.length1 - win_length + 1);
double* winned_ins_probs2 = (double*)malloc(sizeof(double) * global_aln_info.length2 - win_length + 1);
char win_ins_prob_file_name[100];
sprintf(win_ins_prob_file_name, "win_ins_probs1_%d.txt", win_length);
FILE* win_ins_prob_file = fopen(win_ins_prob_file_name, "w");
for(int cnt1 = 1; cnt1 < global_aln_info.length1 - win_length + 1; cnt1++)
{
// cnt1 is the index of starting of current window.
winned_ins_probs1[cnt1] = LOG_OF_ZERO;
// cnt2 is the index in second sequence where window is betweenm i.e.,
// the window is assumed to be inserted between cnt2 and cnt2 + 1.
// however I do not put the constraint that cnt1-1 is not aligned to cnt2 and cnt2 is not aligned to
// cnt1 + win_length + 1.
for(int cnt2 = 1; cnt2 < global_aln_info.length2 + 1; cnt2++)
{
// cur_win_ins_prob includes probability of all enumerations of alignments where
// currently set window is inserted in first sequences.
double cur_win_ins_prob = xlog_mul(global_aln_info.fore_hmm_array->probs[cnt1][cnt2][STATE_INS1], global_aln_info.back_hmm_array->probs[cnt1 + win_length][cnt2][STATE_INS1]);
// Calculate the emission probability of inserted sequence by going over all inserted sequence.
// emit the nucleotides in the inserted sequence is sequence 1.
double int_emit_prob = xlog(1);
for(int emit_cnt = cnt1 + 1; emit_cnt <= cnt1 + win_length; emit_cnt++)
{
double trans_emit_prob;
if(emit_cnt == cnt1 + win_length)
{
trans_emit_prob = get_trans_emit_prob(STATE_INS1, STATE_INS1, emit_cnt, cnt2);
}
else
{
trans_emit_prob = get_trans_emit_prob(STATE_INS1, STATE_INS1, emit_cnt, cnt2);
}
int_emit_prob = xlog_mul(int_emit_prob, trans_emit_prob);
}
cur_win_ins_prob = xlog_mul(cur_win_ins_prob, int_emit_prob);
winned_ins_probs1[cnt1] = xlog_sum(winned_ins_probs1[cnt1], cur_win_ins_prob);
}
fprintf(win_ins_prob_file, "%f ", xlog_div(winned_ins_probs1[cnt1], global_aln_info.op_prob));
}
fprintf(win_ins_prob_file, "\n");
fclose(win_ins_prob_file);
}
double* get_poisson_thresholds(t_chip_seq_chr_data* cur_chr_data,
double target_fdr,
int enrichment_mapped_fragment_length,
int min_thresh,
int max_thresh)
{
if(__DUMP_POISSON_BCKGRND_MSGS__)
{
fprintf(stderr, "Computing Poisson based thresholds %d,..., %d\n", min_thresh, max_thresh);
}
int n_wins = cur_chr_data->n_meg_wins();
double* thresholds_per_win = new double[n_wins+2];
for(int i_win = 0; i_win <= n_wins; i_win++)
{
//thresholds_per_win[i_win] = max_thresh; // Ensure that no peaks are selected at the initialization, this automatically handles the windows for which there is no data.
thresholds_per_win[i_win] = 0;
}
// Count the number of reads per window.
int* n_reads_per_window = get_n_reads_per_window(cur_chr_data->n_meg_wins(), cur_chr_data->chip_seq_fragments);
// For each window, go over the threholds to find the threholds for which the probability is above 95%.
for(int i_win = 0; i_win < n_wins; i_win++)
{
if(n_reads_per_window[i_win] == 0)
{
if(__DUMP_POISSON_BCKGRND_MSGS__)
printf("There are no mapped reads in window %d\n", i_win);
//getc(stdin);
}
if(cur_chr_data->n_uniquely_mappable_nucs_per_meg_win->at(i_win) == 0)
{
if(__DUMP_POISSON_BCKGRND_MSGS__)
printf("There are no uniquely mappable nucleotides in window %d\n", i_win);
//getc(stdin);
}
else
{
// This is the average of poisson distribution for the heights in this window.
double avg_read_depth = (double)(n_reads_per_window[i_win] * enrichment_mapped_fragment_length) / (double)cur_chr_data->n_uniquely_mappable_nucs_per_meg_win->at(i_win);
double lambda = avg_read_depth;
double log_lambda = xlog(lambda);
double log_target_cdf = xlog(1.0 - target_fdr);
// Update the log_cdf value for thresholds smaller than min_threshold.
double current_log_cdf = -1.0 * lambda;
double current_factor = -1.0 * lambda; // This is the probability value differentially updated in CDF computation.
for(int thresh = 1;
thresh < min_thresh;
thresh++)
{
double new_multiplier = xlog_div(log_lambda, xlog((double)thresh));
current_factor = xlog_mul(current_factor, new_multiplier);
current_log_cdf = xlog_sum(current_log_cdf, current_factor);
}
// For thresholds between min and max thresholds, compare the value of (log)CDF with the (log)target FDR.
bool found_thresh = false;
for(int thresh = min_thresh;
thresh <= max_thresh && !found_thresh;
thresh++)
{
double new_multiplier = xlog_div(log_lambda, xlog((double)thresh));
current_factor = xlog_mul(current_factor, new_multiplier);
current_log_cdf = xlog_sum(current_log_cdf, current_factor);
if(current_log_cdf > log_target_cdf)
{
found_thresh = true;
thresholds_per_win[i_win] = thresh; // Set the threshold in this window.
}
} // thresh loop.
if(thresholds_per_win[i_win] > 0)
{
if(__DUMP_POISSON_BCKGRND_MSGS__)
fprintf(stderr, "Window %d: %lf\n", i_win, thresholds_per_win[i_win]);
}
} // Check for positive number of reads in the window.
} // i_win loop.
delete [] n_reads_per_window;
// Return the list of threshold arrays.
return(thresholds_per_win);
}
