updated parameters for logit function; add inverse logit when printing summary (40448f9c) · Commits · github_fork / Chromap

src/mapping_parameters.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -27,7 +27,7 @@ struct MappingParameters {
		double cache_update_param = 0.01;
		int cache_size = 4000003;
		bool debug_cache = false;
		std::string frip_est_params = "0.2809;0.8921;7.490e-06;-1.893e-05;-2.178e-05";
		std::string frip_est_params = "0.2771;0.9153;6.0499e-06;-6.1495e-05;-5.8978e-05";
		bool output_num_uniq_cache_slots = true;
		int k_for_minhash = 250;

+10 −5

Original line number	Diff line number	Diff line
		@@ -5,6 +5,7 @@

		#include <stdio.h>
		#include <stdint.h>
		#include <cmath>

		#include "khash.h"
		#include "utils.h"
		@@ -43,6 +44,10 @@ class SummaryMetadata {
		kh_destroy(k64_barcode_metadata, barcode_metadata_);
		}

		inline double inverse_logit(double frip) {
		return (1.0/(1.0 + std::exp(-frip)));
		}

		inline void OutputCounts(const char barcode, const int counts, FILE *fp, std::vector<double> frip_est_coeffs, bool output_num_cache_slots_info)
		{
		// define variables to store values
		@@ -59,11 +64,11 @@ class SummaryMetadata {
		size_t num_cache_slots = counts[SUMMARY_METADATA_CARDINALITY];

		// compute the estimated frip
		double est_frip = (fric != 0.0) ? frip_est_coeffs[0] + /* constant */
		double est_frip = (fric != 0.0) ? inverse_logit(frip_est_coeffs[0] + /* constant */
		(frip_est_coeffs[1] * fric) +
		(frip_est_coeffs[2] * num_dup) +
		(frip_est_coeffs[3] * num_unmapped) +
		(frip_est_coeffs[4] * num_lowmapq) : 0.0;
		(frip_est_coeffs[4] * num_lowmapq)) : 0.0;

		// print out data for current barcode
		if (!output_num_cache_slots_info) {