<commit_before>/*
 * This file is part of quip.
 *
 * Copyright (c) 2012 by <NAME> <<EMAIL>>
 *
 */


#include "config.h"
#include "quip.h"
#include "assembler.h"
#include "kmer.h"
#include "misc.h"
#include "quip_parse.h"
#include <getopt.h>
#include <errno.h>
#include <stdbool.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <inttypes.h>
#include <unistd.h>
#include <fcntl.h>
#ifndef O_BINARY
#define O_BINARY 0
#endif 

const char* prog_name;


bool force_flag      = false;
bool quick_flag      = false;
bool stdout_flag     = false;

enum {
    QUIP_CMD_COMPRESS,
    QUIP_CMD_DECOMPRESS,
    QUIP_CMD_LIST,
    QUIP_CMD_TEST
} quip_cmd = QUIP_CMD_COMPRESS;

void print_help()
{
    printf(
"Usage: quip [OPTION]... [FILE]...\n"
"Compress or decompress FASTQ sequence files with extreme prejudice.\n\n"
"  -d, --decompress   decompress\n"
"  -t, --test         test compressed file integrity\n"
"  -l, --list         list total number of reads and bases\n"
"  -c, --stdout       write on standard output\n"<commit_msg>Include a sys/stat.h, necessary on some systems.<commit_after>/*
 * This file is part of quip.
 *
 * Copyright (c) 2012 by <NAME> <<EMAIL>>
 *
 */


#include "config.h"
#include "quip.h"
#include "assembler.h"
#include "kmer.h"
#include "misc.h"
#include "quip_parse.h"
#include <getopt.h>
#include <errno.h>
#include <stdbool.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <inttypes.h>
#include <unistd.h>
#include <fcntl.h>
#include <sys/stat.h>
#ifndef O_BINARY
#define O_BINARY 0
#endif 

const char* prog_name;


bool force_flag      = false;
bool quick_flag      = false;
bool stdout_flag     = false;

enum {
    QUIP_CMD_COMPRESS,
    QUIP_CMD_DECOMPRESS,
    QUIP_CMD_LIST,
    QUIP_CMD_TEST
} quip_cmd = QUIP_CMD_COMPRESS;

void print_help()
{
    printf(
"Usage: quip [OPTION]... [FILE]...\n"
"Compress or decompress FASTQ sequence files with extreme prejudice.\n\n"
"  -d, --decompress   decompress\n"
"  -t, --test         test compressed file integrity\n"
"  -l, --list         list total number of reads and bases\n"
"  -c, --stdout       write on standard output\n"
{'fraction_non_alphanumeric': 0.14259173246632606, 'fraction_numerical': 0.004644681839294009, 'mean_word_length': 3.325301204819277, 'pattern_counts': {'":': 0, '<': 28, '<?xml version=': 0, '>': 28, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2910066', 'n_tokens_mistral': 868, 'n_tokens_neox': 831, 'n_words': 223}