<commit_before>require 'yaml'

task_params = YAML.load_file('task_params.yaml')

min_affinity_change = task_params[:fold_change_cutoff]
max_relevant_pvalue = task_params[:pvalue_cutoff]

command = ["java -cp ape.jar ru.autosome.perfectosape.SNPScan collection snp_list.txt --precalc collection_precalc",
            "--pvalue-cutoff #{max_relevant_pvalue}",
            "--fold-change-cutoff #{min_affinity_change}",
            "-b wordwise"
          ].join(' ')

puts command

File.write('task_result.txt', SMBSMCore.soloist(command, $ticket))<commit_msg>fix shell command to join arguments<commit_after>require 'yaml'
require 'shellwords'

task_params = YAML.load_file('task_params.yaml')

min_affinity_change = task_params[:fold_change_cutoff]
max_relevant_pvalue = task_params[:pvalue_cutoff]

command = ["java -cp ape.jar ru.autosome.perfectosape.SNPScan collection snp_list.txt --precalc collection_precalc",
            "--pvalue-cutoff #{max_relevant_pvalue}",
            "--fold-change-cutoff #{min_affinity_change}",
            "-b wordwise"
          ].shelljoin

puts command

File.write('task_result.txt', SMBSMCore.soloist(command, $ticket))
{'fraction_non_alphanumeric': 0.12424503882657463, 'fraction_numerical': 0.0, 'mean_word_length': 4.296803652968037, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, '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': '3499022', 'n_tokens_mistral': 393, 'n_tokens_neox': 376, 'n_words': 64}