utils.h

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// Utility functions
 
#ifndef UTILS_H
#define UTILS_H
 
#include <htslib/sam.h>
#include <htslib/synced_bcf_reader.h>
 
#include <string>
#include <mutex>
#include <chrono>
 
 
// Guard to close the BAM file
// struct BamFileGuard {
//     samFile* fp_in;
//     hts_idx_t* idx;
//     bam_hdr_t* bamHdr;
 
//     BamFileGuard(samFile* fp_in, hts_idx_t* idx, bam_hdr_t* bamHdr)
//         : fp_in(fp_in), idx(idx), bamHdr(bamHdr) {}
 
//     ~BamFileGuard() {
//         if (idx) {
//             hts_idx_destroy(idx);
//             idx = nullptr;
//         }
//         if (bamHdr) {
//             bam_hdr_destroy(bamHdr);
//             bamHdr = nullptr;
//         }
//         if (fp_in) {
//             sam_close(fp_in);
//             fp_in = nullptr;
//         }
//     }
 
//     BamFileGuard(const BamFileGuard&) = delete;  // Non-copyable
//     BamFileGuard& operator=(const BamFileGuard&) = delete;  // Non-assignable
// };
 
// Print the progress of a task
void printProgress(int progress, int total);
 
// Run bcftools to determine the chr notation of a VCF file
bool isChrNotation(std::string vcf_filepath);
 
// Print a message to stdout in a thread-safe manner
void printMessage(std::string message);
 
// Print an error message to stderr in a thread-safe manner
void printError(std::string message);
 
std::string getElapsedTime(std::chrono::high_resolution_clock::time_point start, std::chrono::high_resolution_clock::time_point end);
 
std::string removeChrPrefix(std::string chr);
 
void printMemoryUsage(const std::string &functionName);
 
bool fileExists(const std::string &filepath);
 
bool isFileEmpty(const std::string &filepath);
 
void closeJSON(const std::string & filepath);
 
#endif // UTILS_H