Removed unused demultiplexing code

src/demultiplexing.cpp

-#include "demultiplexing.h"
-
-KSEQ_INIT(gzFile, gzread) // Kseq init macro
-
-void demultiplexing(Parameters &parameters) {
-
-    /* Demultiplexing is actually not a trivial task if done correctly.
-     * It may get implemented later but for now this pipeline relies on Stacks for this step.
-     */
-
-    const std::string sbf1 = "TGCA";
-
-    const std::unordered_map<std::string, std::string> barcodes = load_barcodes(parameters);
-
-    std::string par = "output_dir_path";
-    std::string output_dir_path = parameters.get_value_from_name<std::string>(par);
-
-    std::ofstream log_file(output_dir_path + "demultiplexing.log");
-    std::ofstream summary_file(output_dir_path + "summary.tsv");
-
-    std::unordered_map<std::string, uint64_t> statistics;
-
-    std::unordered_map<std::string, gzFile> output_files;
-
-    // Output files are mapped to their barcodes.
-    std::string output_file_path;
-    for (auto b: barcodes) {
-        output_file_path = output_dir_path + b.second + ".fq.gz";
-        // Create a compressed output file, the number after wb indicates the level of compression (1 -> low, 9 -> high)
-        output_files[b.first] = gzopen(output_file_path.c_str(), "wb9");
-        if(!output_files[b.first]) std::cout << std::endl << "** Error: could not open output file \"" << output_file_path << "\"" << std::endl;
-    }
-
-    gzFile input_file;
-    kseq_t* sequence; // Create the seq object
-    int line_n; // Stores the length of a line
-    std::string revcomp = "";
-    char nuc = 'A';
-    uint count;
-
-    par = "input_file_path";
-    input_file = gzopen(parameters.get_value_from_name<std::string>(par).c_str(), "r");
-    sequence = kseq_init(input_file); // Initialize the seq object
-
-    // Read through the file and store the results
-    while ((line_n = kseq_read(sequence)) >= 0) {
-        rev_comp(sequence->seq.s, revcomp, nuc);
-        ++count;
-    }
-
-    kseq_destroy(sequence); // Destroy the seq object
-    gzclose(input_file);
-
-    // Close all output files
-    for(auto& ofile: output_files) {
-        gzclose(ofile.second);
-    }
-}

src/demultiplexing.h

-#pragma once
-#include <string>
-#include <vector>
-#include <fstream>
-#include <unordered_map>
-#include <unordered_set>
-#include <zlib.h>
-#include "utils.h"
-#include "parameters.h"
-#include "barcodes_file.h"
-#include "kseq/kseq.h"
-
-
-// Main function implementing the analysis
-void demultiplexing(Parameters& parameters);

src/radsex.h

@@ -6,7 +6,6 @@
 #include "process_reads.h"
 #include "subset.h"
 #include "frequencies.h"
-#include "demultiplexing.h"
 #include "group_loci.h"
 #include "significant_sequences.h"
 #include "mapping.h"