common.h

#ifndef COMMON_H
#define COMMON_H
#include "htslib/sam.h"
#include <algorithm>
#include <array>
#include <cstdint>
#include <fstream>
#include <iostream>
#include <list>
#include <sstream>
#include <string>
#include <unordered_map>
#include <vector>

// global definitions/constants
#define VERSION "0.0.6"

// definitions/constants for argparsing
#define DEFAULT_MIN_QUAL 20
#define DEFAULT_MIN_DEPTH 10
#define DEFAULT_MIN_FREQ 0.5
#define DEFAULT_AMBIG 'N'
#define DEFAULT_PRIMER_OFFSET 0
#define MESSAGE_MISSING_REQUIRED_ARG "Missing required argument: "
static std::array<const char* const, 4> const HELP_ARG_STRINGS = {"-h", "--help", "-help", "help"};

// definitions/constants for FASTA loading
#define FASTA_STRING_RESERVE 65536

// definitions/constants for counting
#define COUNT_T uint32_t
#define READ_SEQUENCE_RESERVE 1024
#define INSERTION_RESERVE 32
static const int32_t FAIL_FLAGS = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP;
static const int32_t BASE_TO_NUM[] = {-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0, -1, 1, -1, -1, -1, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0, -1, 1, -1, -1, -1, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1};
static const uint8_t COMPLEMENT[] = {'\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', 'T', '\0', 'G', '\0', '\0', '\0', 'C', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', 'A', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', 'T', '\0', 'G', '\0', '\0', '\0', 'C', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', 'A', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0'};

// transform a string to its reverse complement in-place
void rev_comp_inplace(std::string & s);

#endif