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/*
@copyright 2016-2021 Clarity Genomics BVBA
@copyright 2012-2016 Bonsai Bioinformatics Research Group
@copyright 2014-2016 Knight Lab, Department of Pediatrics, UCSD, La Jolla
@parblock
SortMeRNA - next-generation reads filter for metatranscriptomic or total RNA
This is a free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
SortMeRNA is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License
along with SortMeRNA. If not, see <http://www.gnu.org/licenses/>.
@endparblock
@contributors Jenya Kopylova jenya.kopylov@gmail.com
Laurent Noé laurent.noe@lifl.fr
Pierre Pericard pierre.pericard@lifl.fr
Daniel McDonald wasade@gmail.com
Mikaël Salson mikael.salson@lifl.fr
Hélène Touzet helene.touzet@lifl.fr
Rob Knight robknight@ucsd.edu
*/
/** @file common.hpp */
#pragma once
#include <string>
#include <sstream>
#include <iostream> // std::cout
#include <sys/time.h>
#include "config.h"
#if defined(_WIN32)
# include "windows.h"
# include "psapi.h"
#else
# include <fstream>
#endif
const char FASTA_HEADER_START = '>';
const char FASTQ_HEADER_START = '@';
const std::string FWD = "FWD";
const std::string REV = "REV";
enum class BIO_FORMAT : unsigned { FASTQ = 0, FASTA = 1 };
enum class ZIP_FORMAT : unsigned { GZIP = 0, ZLIB = 1, FLAT = 2, XPRESS = 3 };
enum class FEED_TYPE : unsigned { SPLIT_READS = 0, LOCKLESS = 1, MAX = LOCKLESS };
enum class BlastFormat { TABULAR, REGULAR}; // format of the Blast output
/*! @brief Map nucleotides to integers.
Ambiguous letters map to 4.
{A/a,C/c,G/g,T/t,U/u} = {0,1,2,3,3} respectively.
*/
const char nt_table[128] = {
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
};
// see old paralleltraversal.cpp::format_rev
const char rc_table[128] = {
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 3, 4, 2, 4, 4, 4, 1, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 0, 0, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 3, 4, 2, 4, 4, 4, 1, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 0, 0, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
};
const char nt_map[5] = { 'A', 'C', 'G', 'T', 'N' };
const char complement[5] = { 3, 2, 1, 0, 4 }; // A <-> T, C <-> G, N <-> N
extern timeval t;
/*! @brief Macro for timing */
#define TIME(x) gettimeofday(&t, NULL); x = t.tv_sec + (t.tv_usec/1000000.0);
/*! @brief start color text red */
#if defined(_WIN32)
# define RED ""
# define GREEN ""
# define YELLOW ""
# define BLUE ""
# define BOLD ""
# define UNDL ""
# define COLOFF ""
const char DELIM = ';';
#else
# define RED "\033[0;31m"
# define GREEN "\033[0;32m"
# define YELLOW "\033[0;33m"
# define BLUE "\033[0;34m"
# define BOLD "\033[1m"
# define UNDL "\033[4m" // underline
# define COLOFF "\033[0m" // color off
const char DELIM = ':';
#endif
/*! @brief Maximum length of input reads
(not limited to this length algorithmically)
*/
#define MAX_READ_LEN 30000
//#define LOCKQUEUE // Lock queue with mutexes
#define CONCURRENTQUEUE // lockless queue
#define STAMP "[" << __func__ << ":" << __LINE__ << "] "
#define STAMPL "[" << __FILE__ << ":" << __func__ ":" << __LINE__ << "] "
template<typename ...Args>
static inline std::string fold_to_string(Args&&... args) {
std::stringstream ss;
(ss << ... << args);
return ss.str();
}
// https://stackoverflow.com/questions/63166/how-to-determine-cpu-and-memory-consumption-from-inside-a-process
#if defined(_WIN32)
static inline size_t get_memory() {
PROCESS_MEMORY_COUNTERS_EX pmc;
GetProcessMemoryInfo(GetCurrentProcess(), (PROCESS_MEMORY_COUNTERS*)&pmc, sizeof(pmc));
return pmc.PrivateUsage; // process Commit memory (== Resource Monitor:Commit)
}
#else
/*
* amount of memory that have been mapped into the process' address space
* cat /proc/self/status | grep 'VmRSS:'
* 'VmRSS: 336 kB'
*/
static inline size_t get_memory() {
std::ifstream ifs("/proc/self/status", std::ios::binary);
size_t mem = 0;
if (ifs.is_open()) {
for (std::string line; std::getline(ifs, line); ) {
unsigned pos_start = 0;
unsigned pos_end = 0;
if (line.find("VmRSS:") != std::string::npos) {
for (unsigned i = 0; i < line.length(); ++i) {
if (pos_start == 0) {
if (std::isdigit(line[i]))
pos_start = i;
}
else {
if (pos_end == 0 && !std::isdigit(line[i])) {
pos_end = i;
break;
}
}
}
if (pos_end > pos_start) {
std::string mstr = line.substr(pos_start, pos_end + 1 - pos_start);
mem = std::atoi(mstr.data());
}
}
}
}
return mem;
}
#endif
#define INFO(...) \
{\
std::stringstream ss; \
ss << STAMP << fold_to_string(__VA_ARGS__) << std::endl; \
std::cout << ss.str(); \
}
// no end line
#define INFO_NE(...) \
{\
std::stringstream ss; \
ss << STAMP << fold_to_string(__VA_ARGS__); \
std::cout << ss.str(); \
}
// No Stamp, no endl
#define INFO_NS(...) \
{\
std::stringstream ss; \
ss << fold_to_string(__VA_ARGS__); \
std::cout << ss.str(); \
}
#define INFO_MEM(...) \
{\
std::stringstream ss; \
ss << STAMP << fold_to_string(__VA_ARGS__) << " Memory KB: " << (get_memory() >> 10) << std::endl; \
std::cout << ss.str();\
}
#define WARN(...) \
{\
std::stringstream ss; \
ss << '\n' << STAMP << YELLOW << "WARNING" << COLOFF << ": " << fold_to_string(__VA_ARGS__) << std::endl; \
std::cout << ss.str();\
}
#define ERR(...) \
{\
std::stringstream ss; \
ss << '\n' << STAMP << RED << "ERROR" << COLOFF << ": " << fold_to_string(__VA_ARGS__) << std::endl; \
std::cerr << ss.str();\
}
#define PRN_MEM(msg) \
{\
std::stringstream ss; \
ss << STAMP << msg << " Memory KB: " << (get_memory() >> 10) << std::endl; \
std::cout << ss.str();\
}
#define PRN_MEM_TIME(msg, time) \
{\
std::stringstream ss; \
ss << STAMP << msg << " Memory KB: " << (get_memory() >> 10) << " Elapsed sec: " << time << std::endl; \
std::cout << ss.str();\
}
//~EOF
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