// Created by Saliya Ekanayake on 12/17/18.

#pragma once

#include <iosfwd>



namespace
pastis
{

extern const char *PROGRAM_NAME;

extern const char *CMD_OPTION_INPUT;
extern const char *CMD_OPTION_DESCRIPTION_INPUT;

extern const char *CMD_OPTION_INPUT_SEQ_COUNT;
extern const char *CMD_OPTION_DESCRIPTION_INPUT_SEQ_COUNT;

extern const char *CMD_OPTION_INPUT_OVERLAP;
extern const char *CMD_OPTION_DESCRIPTION_INPUT_OVERLAP;

extern const char *CMD_OPTION_SEED_COUNT;
extern const char *CMD_OPTION_DESCRIPTION_SEED_COUNT;

extern const char *CMD_OPTION_KMER_LENGTH;
extern const char *CMD_OPTION_DESCRIPTION_KMER_LENGTH;

extern const char *CMD_OPTION_GAP_OPEN;
extern const char *CMD_OPTION_DESCRIPTION_GAP_OPEN;

extern const char *CMD_OPTION_GAP_EXT;
extern const char *CMD_OPTION_DESCRIPTION_GAP_EXT;

extern const char *CMD_OPTION_KMER_STRIDE;
extern const char *CMD_OPTION_DESCRIPTION_KMER_STRID;

extern const char *CMD_OPTION_OVERLAP_FILE;
extern const char *CMD_OPTION_DESCRIPTION_OVERLAP_FILE;

extern const char *CMD_OPTION_ALIGN_FILE;
extern const char *CMD_OPTION_DESCRIPTION_ALIGN_FILE;

extern const char *CMD_OPTION_NO_ALIGN;
extern const char *CMD_OPTION_DESCRIPTION_NO_ALIGN;

extern const char *CMD_OPTION_FULL_ALIGN;
extern const char *CMD_OPTION_DESCRIPTION_FULL_ALIGN;

extern const char *CMD_OPTION_XDROP_ALIGN;
extern const char *CMD_OPTION_DESCRIPTION_XDROP_ALIGN;

extern const char *CMD_OPTION_BANDED_ALIGN;
extern const char *CMD_OPTION_DESCRIPTION_BANDED_ALIGN;

extern const char *CMD_OPTION_GPUBSW_ALIGN;
extern const char *CMD_OPTION_DESCRIPTION_GPUBSW_ALIGN;

extern const char *CMD_OPTION_IDX_MAP;
extern const char *CMD_OPTION_DESCRIPTION_IDX_MAP;

extern const char *CMD_OPTION_ALPH;
extern const char *CMD_OPTION_DESCRIPTION_ALPH;

extern const char *CMD_OPTION_SUBS;
extern const char *CMD_OPTION_DESCRIPTION_SUBS;

extern const char *CMD_OPTION_JOB_NAME_PREFIX;
extern const char *CMD_OPTION_DESCRIPTION_JOB_NAME_PREFIX;

extern const char *CMD_OPTION_LOG_FREQ;
extern const char *CMD_OPTION_DESCRIPTION_LOG_FREQ;

extern const char *CMD_OPTION_AF_FREQ;
extern const char *CMD_OPTION_DESCRIPTION_AF_FREQ;

extern const char *CMD_OPTION_CKTHR;
extern const char *CMD_OPTION_DESCRIPTION_CKTHR;

extern const char *CMD_OPTION_MOSTHR;
extern const char *CMD_OPTION_DESCRIPTION_MOSTHR;

extern const char *CMD_OPTION_ALN_BATCH_SZ;
extern const char *CMD_OPTION_DESCRIPTION_ALN_BATCH_SZ;

extern const char *CMD_OPTION_SIM_BR;
extern const char *CMD_OPTION_DESCRIPTION_SIM_BR;

extern const char *CMD_OPTION_SIM_BC;
extern const char *CMD_OPTION_DESCRIPTION_SIM_BC;

extern const char *CMD_OPTION_LB;
extern const char *CMD_OPTION_DESCRIPTION_LB;

extern const char *CMD_OPTION_STATS;
extern const char *CMD_OPTION_DESCRIPTION_STATS;

}
