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code cleanup & small changes in stats calc
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‎.github/workflows/docker.yml

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- name: extract version
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id: extract_version
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run: |
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VERSION=$(grep 'ARG VERSION=' Dockerfile | cut -d'=' -f2)
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VERSION=${GITHUB_REF#refs/tags/}
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echo "::set-output name=VERSION::$VERSION"
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- name: build and push

‎CHANGELOG.md

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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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# [0.2.2]
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## Features
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- add test data
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## Fix
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- Code cleanup
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- Fix in writing to stats.txt that cause overwriting in different subcalls
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# [0.2.1]
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## Features

‎CMakeLists.txt

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cmake_minimum_required(VERSION 3.22.1)
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project(RNAnue VERSION 0.2.1)
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project(RNAnue VERSION 0.2.2)
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set(CMAKE_CXX_STANDARD 20)
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set(CMAKE_CXX_STANDARD_REQUIRED True)
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set(CMAKE_CXX_FLAGS -fopenmp)

‎README.md

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[![docker-release](https://github.com/Ibvt/RNAnue/actions/workflows/docker.yml/badge.svg)](https://github.com/Ibvt/RNAnue/actions/workflows/docker.yml)
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# RNAnue - 0.2.1
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# RNAnue - 0.2.2
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## About
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RNAnue is a comprehensive analysis to detect RNA-RNA interactions from Direct-Duplex-Detection (DDD) data.
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### Interaction table
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The `analysis` procedure generates `_interactions` files for each library in
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which each line represents an annotated split read that is mapped to a
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transcript interaction. The fields are defined as follows:
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The `analysis` procedure generates `_interactions` files for each library in which each line represents an annotated
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split read that is mapped to a transcript interaction. The fields are defined as follows:
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| Field | Description |
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| ----- | ----------- |
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| mfe | Hybridisation energy of the interaction |
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| mfe_struc | Minimum free energy (MFE) structure of interaction in dot-bracket notation |
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The main result of an RNAnue analysis are transcript interactions.
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They are stored in the file `allints.txt` in the same directory.
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Its entries are structured as described in the following where
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columns with prefix <sample> are given for each sample specified in
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the analysis (within the same file).
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The main result of an RNAnue analysis are transcript interactions. They are stored in the file `allints.txt` in the
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same directory. Its entries are structured as described in the following where columns with prefix <sample> are given
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for each sample specified in the analysis (within the same file).
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| Field | Description |
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|-----------------------| ----------- |
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each step of the analysis.
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### Docker
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In additon, we provide a ready-to-use Docker container that has RNAnue preconfigured.
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https://hub.docker.com/repository/docker/cobirna/rnanue
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In additon, we provide a ready-to-use [Docker container](https://hub.docker.com/repository/docker/cobirna/rnanue) that
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has RNAnue preconfigured.
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### Testing
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We provide a test dataset in the [test](./test/data/) folder that can be used to test the installation.
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# Troubleshooting
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contact [email protected] or create an issue

‎include/Analysis.hpp

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#include <boost/program_options.hpp>
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#include <boost/filesystem.hpp>
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#include <boost/property_tree/ptree.hpp>
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#include <boost/property_tree/json_parser.hpp>
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#include <boost/accumulators/accumulators.hpp>
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#include <boost/accumulators/statistics.hpp>
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#include <boost/math/distributions/binomial.hpp>
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#include <boost/math/distributions/chi_squared.hpp>
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// SeqAn3
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#include <seqan3/io/sam_file/all.hpp>
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#include <seqan3/core/debug_stream.hpp>
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// Class
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#include "IBPTree.hpp"
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#include "Stats.hpp"
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// define tags
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using seqan3::operator""_tag;
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namespace po = boost::program_options;
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namespace fs = boost::filesystem;
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namespace pt = boost::property_tree;
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namespace jp = boost::property_tree::json_parser;
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namespace ma = boost::math;
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class Analysis {
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void normalize(); // normalize the frequencies to 1
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// write output files (of the analysis)
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void writeStats();
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void writeInteractionsHeader(std::ofstream& fout);
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void writeAllIntsHeader(std::ofstream& fout);
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void addToAllIntsHeader(std::ofstream& fout, std::string key);
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void writeAllIntsHeader(std::vector<int> condLastFlag, std::ofstream& fout);
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void writeAllInts();
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void writeAllIntsCounts();
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void writeAllIntsJGF();
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// other operations
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void addToFreqMap(std::pair<std::string,std::string> key, double value);
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double calcGCS(std::vector<double>& complementarities);
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double calcGHS(std::vector<double>& hybenergies);
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double calcStat(dtp::IntKey key, int x);
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double calcAdjusted(std::vector<double>& values);
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private:
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po::variables_map params;
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IBPTree features;
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std::map<std::pair<std::string,std::string>,double> freq; // strand, name
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std::string condition; // buffers the current condition
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// maps for storing filters and suppreads
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std::vector<std::string> conditions; // buffers all conditions
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// maps for storing filters and suppreads (and other information)
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std::map<dtp::IntKey, std::vector<double>> suppreads;
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std::map<dtp::IntKey, std::vector<std::vector<double>>> complementarities;
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std::map<dtp::IntKey, std::vector<std::vector<double>>> hybenergies;
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// Stats
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std::shared_ptr<Stats> stats;
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int repcount; // counter for current replicate
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int readcount; // total number of reads
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std::vector<int> repcountCond; // number of replicates per condition
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};
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#endif //RNANUE_ANALYSIS_HPP

‎include/DataTypes.hpp

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int alignedCount;
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int splitsCount;
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int multSplitsCount;
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int nSurvivedCount;
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int interactionsCount;
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StatsFields() : readsCount(0), alignedCount(0), splitsCount(0), multSplitsCount(0), interactionsCount(0) {}
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StatsFields(int readsCount, int alignedCount, int splitsCount, int multSplitsCount) :
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readsCount(readsCount), alignedCount(alignedCount), splitsCount(splitsCount),
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multSplitsCount(multSplitsCount), interactionsCount(0) {} // constructor for analysis class
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};
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using StatsMap = std::map<std::string, StatsFields>;
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using StatsMap = std::map<std::string, std::vector<StatsFields>>;
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using SpliceJunctions = std::map<std::string, std::vector<std::pair<size_t,size_t>>>;
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// Analysis

‎include/SplitReadCalling.hpp

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void addComplementarityToSamRecord(SAMrecord &rec1, SAMrecord &rec2, TracebackResult &res);
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void addHybEnergyToSamRecord(SAMrecord &rec1, SAMrecord &rec2, double &hyb);
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void writeSAMrecordToBAM(auto& bamfile, std::vector<std::pair<SAMrecord, SAMrecord>>& records);
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void writeStats();
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private:
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po::variables_map params;
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IBPTree features;
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//Stats stats;
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std::shared_ptr<Stats> stats;
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int replPerCond; // number of replicates per condition
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std::string condition; // stores the current condition
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std::deque<std::string> refIds; // stores the reference ids
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FilterScores filterScores;

‎include/Stats.hpp

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class Stats {
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public:
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Stats();
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Stats(std::string statsFile);
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// Move constructor / no needed because its unique
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Stats(Stats&& other) noexcept : stats(other.stats) {}
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Stats& operator=(const Stats&) = delete;
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// getter & setter
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void setReadsCount(std::string condition, int increment);
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void setAlignedCount(std::string condition, int increment);
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void setSplitsCount(std::string condition, int increment);
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void setMultSplitsCount(std::string condition, int increment);
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void setReadsCount(std::string condition, int repl, int increment);
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void setAlignedCount(std::string condition, int repl, int increment);
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void setSplitsCount(std::string condition, int repl, int increment);
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void setMultSplitsCount(std::string condition, int repl, int increment);
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void setInteractionsCount(std::string condition, int repl, int increment);
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void reserveStats(std::string condition, int repl); // creates new entry for replicate
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// write stats back to file
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void writeStats(fs::path outdir);
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void writeStats(fs::path outdir, std::string subcall);
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dtp::StatsMap stats;

‎include/Utility.hpp

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#include <iostream>
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#include <iomanip>
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#include <chrono>
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#include <random>
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// Boost
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#include <boost/filesystem.hpp>
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bool withinRange(int a, int b, int range);
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std::string removeNonPrintable(const std::string str);
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std::string getTime(); // reports the current time
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std::vector<int> lastOccFlag(std::vector<std::string>& vec);
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}
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namespace stats {
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double median(std::vector<double>& values);
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double randNum(double min, double max);
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}
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// sequence input/output

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