<commit_before><?xml version="1.0"?>
<tool_dependency>
    <package name="trinity" version="2.1.1">
        <repository name="package_trinity_2_1_1" owner="iuc" />
    </package>
    <package name="bowtie" version="1.1.2">
        <repository name="package_bowtie_1_1_2" owner="iuc" />
    </package>
    <package name="bowtie2" version="2.2.6">
        <repository name="package_bowtie_2_2_6" owner="iuc" />
    </package>
    <package name="samtools" version="1.2">
        <repository name="package_samtools_1_2" owner="iuc" />
    </package>
    <package name="edger" version="3.12.0">
        <repository name="package_r_edger_3_12_0" owner="iuc" />
    </package>
    <package name="rsem" version="1.2.28">
        <repository name="package_rsem_1_2_28" owner="iuc" />
    </package>
    <package name="express" version="1.5.1">
        <repository name="package_express_1_5_1" owner="iuc" />
    </package>
    <package name="limma" version="3.28.2">
        <repository name="package_r_limma_3_28_2" owner="iuc" />
    </package>
    <package name="deseq2" version="1.10.0">
       <repository name="package_deseq2_1_10_0" owner="iuc" />
    </package>
    <set_environment version="1.0">
        <environment_variable name="TRINITY_MEM_OPTIONS" action="set_to">"--max_memory 30G --bflyHeapSpaceMax 30G"</environment_variable>
    </set_environment>
</tool_dependency><commit_msg>50% decrease on the number of quotes<commit_after><?xml version="1.0"?>
<tool_dependency>
    <package name="trinity" version="2.1.1">
        <repository name="package_trinity_2_1_1" owner="iuc" />
    </package>
    <package name="bowtie" version="1.1.2">
        <repository name="package_bowtie_1_1_2" owner="iuc" />
    </package>
    <package name="bowtie2" version="2.2.6">
        <repository name="package_bowtie_2_2_6" owner="iuc" />
    </package>
    <package name="samtools" version="1.2">
        <repository name="package_samtools_1_2" owner="iuc" />
    </package>
    <package name="edger" version="3.12.0">
        <repository name="package_r_edger_3_12_0" owner="iuc" />
    </package>
    <package name="rsem" version="1.2.28">
        <repository name="package_rsem_1_2_28" owner="iuc" />
    </package>
    <package name="express" version="1.5.1">
        <repository name="package_express_1_5_1" owner="iuc" />
    </package>
    <package name="limma" version="3.28.2">
        <repository name="package_r_limma_3_28_2" owner="iuc" />
    </package>
    <package name="deseq2" version="1.10.0">
       <repository name="package_deseq2_1_10_0" owner="iuc" />
    </package>
    <set_environment version="1.0">
        <environment_variable name="TRINITY_MEM_OPTIONS" action="set_to">'--max_memory 30G --bflyHeapSpaceMax 30G'</environment_variable>
    </set_environment>
</tool_dependency>
{'fraction_non_alphanumeric': 0.1711325473383351, 'fraction_numerical': 0.05144694533762058, 'mean_word_length': 3.819277108433735, 'pattern_counts': {'":': 0, '<': 71, '<?xml version=': 2, '>': 71, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, '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': '2474210', 'n_tokens_mistral': 1038, 'n_tokens_neox': 1000, 'n_words': 157}