<commit_before>#!/bin/bash

# Usage info
usage() {
        echo "Usage: ./${0##*/} --input <INPUT> [ --length <INT> ] [--gap_extension <INT> ] [ --threads <INT> ] [ -h ]"
}
show_help() {
        usage
        cat << EOF
Use the GEM-library (installed in your \$PATH) and a gap correction for obtain the callable genome.
	
	Options:
        -h  | --help	display this help and exit
        -i  | --input <INPUT>	FASTA file to compute the callable genome
        -l  | --length <INT>	read length for the mapping [default=100]
        -g  | --gap_extension <INT>	expand the gap regions INT bp
        -t  | --threads <INT>	number of threads to use with gem-mappability [default=2]
EOF
}

# function for check the error
checkError() {
	if [ $1 -ne 0 ]; then
		echo "Unexpected error running the pipeline"
		exit 1
	fi
}

# Default values
length=100
threads=2
gap=5

# Parsing command line
while [ $# -ne 0 ];
do
	opt=$1
	shift
	case "$opt" in
		"-h" | "--help"			 )	show_help 1>&2
									exit 0
									;;
		"-i" | "--input"		 )	input=$1
									shift<commit_msg>added default gap_extension and change permissions<commit_after>#!/bin/bash

# Usage info
usage() {
        echo "Usage: ./${0##*/} --input <INPUT> [ --length <INT> ] [--gap_extension <INT> ] [ --threads <INT> ] [ -h ]"
}
show_help() {
        usage
        cat << EOF
Use the GEM-library (installed in your \$PATH) and a gap correction for obtain the callable genome.
	
	Options:
        -h  | --help	display this help and exit
        -i  | --input <INPUT>	FASTA file to compute the callable genome
        -l  | --length <INT>	read length for the mapping [default=100]
        -g  | --gap_extension <INT>	expand the gap regions INT bp [default=5]
        -t  | --threads <INT>	number of threads to use with gem-mappability [default=2]
EOF
}

# function for check the error
checkError() {
	if [ $1 -ne 0 ]; then
		echo "Unexpected error running the pipeline"
		exit 1
	fi
}

# Default values
length=100
threads=2
gap=5

# Parsing command line
while [ $# -ne 0 ];
do
	opt=$1
	shift
	case "$opt" in
		"-h" | "--help"			 )	show_help 1>&2
									exit 0
									;;
		"-i" | "--input"		 )	input=$1
									shift
{'fraction_non_alphanumeric': 0.13851817763460653, 'fraction_numerical': 0.017947537965945698, 'mean_word_length': 2.3089802130898023, 'pattern_counts': {'":': 0, '<': 23, '<?xml version=': 0, '>': 21, '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': '5279206', 'n_tokens_mistral': 841, 'n_tokens_neox': 726, 'n_words': 267}