<commit_before>#!/usr/bin/env perl
#------------------------------------------------------------------------------#
# global chloroExtractor options
threads => 8,
reads => [qw()],
mates => [qw()],
out => undef,

#------------------------------------------------------------------------------#
# scale_reads.pl
scr => {
    reads => undef,
    mates => undef,
    out => 'scr', 
    ref_cluster => undef,
    target_coverage => 200,
    min_single_coverage => 20,
    min_covered_CDS => 25,
    coverage_check_interval => 20000,

    # currently only bowtie2 is fully implemented
    # # shrimp (gmapper-ls) options
    # gmapper_ls_path => '/software/shrimp/bin/gmapper-ls',
    # gmapper_ls_log => './shrimp.log',
    # gmapper_ls_params => {
    # 	"--qv-offset" => 33, 
    # 	"--all-contigs" => "",
    # 	"--single-best-mapping" => "",
    # 	"-h" => "95%",
    # 	"--seeds" => "w12",
    # 	"-N" => 10,
    # },

    # bowtie2 options
    bowtie2_path => "/software/bowtie2/",
    bowtie2_DB => undef,
    bowtie2_log => './bowtie2.log',
    bowtie2_params => {
	"--no-unal" => "",
    },
}, 

#------------------------------------------------------------------------------#
# jellyfish reads
jfr => {
    jf_opt => [qw(-m 31 -s 500M -o scr.jf -C)],
    jf_opt2 => [qw(-m 31 -s 500M -o kfr.jf -C)],
    jf_in => [qw(scr_1.fq scr_2.fq)]
    jf_in2 => [qw(kfr_1.fq kfr_2.fq)]
}, 


#------------------------------------------------------------------------------#
# peak_detection.pl
ped => {}, 

<commit_msg>Fixed a typo in global config file<commit_after>#!/usr/bin/env perl
#------------------------------------------------------------------------------#
# global chloroExtractor options
threads => 8,
reads => [qw()],
mates => [qw()],
out => undef,

#------------------------------------------------------------------------------#
# scale_reads.pl
scr => {
    reads => undef,
    mates => undef,
    out => 'scr', 
    ref_cluster => undef,
    target_coverage => 200,
    min_single_coverage => 20,
    min_covered_CDS => 25,
    coverage_check_interval => 20000,

    # currently only bowtie2 is fully implemented
    # # shrimp (gmapper-ls) options
    # gmapper_ls_path => '/software/shrimp/bin/gmapper-ls',
    # gmapper_ls_log => './shrimp.log',
    # gmapper_ls_params => {
    # 	"--qv-offset" => 33, 
    # 	"--all-contigs" => "",
    # 	"--single-best-mapping" => "",
    # 	"-h" => "95%",
    # 	"--seeds" => "w12",
    # 	"-N" => 10,
    # },

    # bowtie2 options
    bowtie2_path => "/software/bowtie2/",
    bowtie2_DB => undef,
    bowtie2_log => './bowtie2.log',
    bowtie2_params => {
	"--no-unal" => "",
    },
}, 

#------------------------------------------------------------------------------#
# jellyfish reads
jfr => {
    jf_opt => [qw(-m 31 -s 500M -o scr.jf -C)],
    jf_opt2 => [qw(-m 31 -s 500M -o kfr.jf -C)],
    jf_in => [qw(scr_1.fq scr_2.fq)],
    jf_in2 => [qw(kfr_1.fq kfr_2.fq)]
}, 


#------------------------------------------------------------------------------#
# peak_detection.pl
ped => {}, 


{'fraction_non_alphanumeric': 0.36933683519369664, 'fraction_numerical': 0.02954694681549573, 'mean_word_length': 1.2927012791572612, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 69, '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': '4849862', 'n_tokens_mistral': 1175, 'n_tokens_neox': 1032, 'n_words': 190}