<commit_before>{
  "tools" : {
    "freebayes" : {
      "description" : "Bayesian variant and haplotype calling",
      "path" : "freebayes/bin",
      "executable" : "freebayes",
      "help" : "--help|-h",
      "arguments" : {
        "--bam" : {
          "short form argument" : "-b",
          "description" : "Add FILE to the set of BAM files to be analyzed.",
          "input" : "true",
          "use for filenames" : "true",
          "output" : "false",
          "resource" : "false",
          "required" : "true",
          "dependent" : "true",
          "extension" : "bam",
          "if input is stream" : "replace",
          "replace argument with" : {
            "argument" : "--stdin",
            "value" : "no value"
          },
          "type" : "string",
          "allow multiple definitions" : "true"
        },
        "--bam-list" : {
          "short form argument" : "-bl",
          "description" : "the input BAM file list.",
          "input" : "true",
          "output" : "false",
          "required" : "false",
          "resource" : "false",
          "dependent" : "true",
          "type" : "string",
          "extension" : "bam",
          "list of input files" : "true",
          "apply by repeating this argument" : "--bam"
        },
        "--vcf" : {
          "short form argument" : "-v",
          "description" : "Output VCF-format results to FILE.",
          "input" : "false",
          "output" : "true",
          "resource" : "false",
          "required" : "true",
          "dependent" : "false",
          "extension" : "vcf",
          "type" : "string",
          "if output to stream" : "do not include"
        },
        "--fasta-reference" : {
          "short form argument" : "-f",
          "description" : "Use FILE as the reference sequence for analysis.",
          "input" : "true",
          "output" : "false",
          "resource" : "true",
          "required" : "true",
          "dependent" : "true",
          "extension" : "fa|fasta",
          "type" : "string"
        },
        "--no-snps" : {
          "short form argument" : "-I",
          "description" : "Ignore SNP alleles.",
          "input" : "false",
          "output" : "false",
          "resource" : "false",
          "required" : "false",
          "dependent" : "false",
          "type" : "flag"
        },
        "--no-indels" : {
          "short form argument" : "-i",
          "description" : "Ignore insertion and deletion alleles.",
          "input" : "false",
          "output" : "false",
          "resource" : "false",
          "required" : "false",
          "dependent" : "false",
          "type" : "flag"
        },
        "--no-mnps" : {
          "short form argument" : "-X",
          "description" : "Ignore multi-nuceotide polymorphisms, MNPs.",
          "input" : "false",
          "output" : "false",
          "resource" : "false",
          "required" : "false",
          "dependent" : "false",
          "type" : "flag"
        },
        "--no-complex" : {
          "short form argument" : "-u",
          "description" : "Ignore complex events (composites of other classes).",
          "input" : "false",
          "output" : "false",
          "resource" : "false",
          "required" : "false",
          "dependent" : "false",
          "type" : "flag"
        },
        "--use-best-n-alleles" : {
          "short form argument" : "-n",
          "description" : "Evaluate only the best N SNP alleles, ranked by sum of supporting quality scores.  (Set to 0 to use all; default: all)",
          "input" : "false",
          "output" : "false",
          "resource" : "false",
          "required" : "false",
          "dependent" : "false",
          "type" : "integer"
        },
        "--max-complex-gap" : {
          "short form argument" : "-E",
          "description" : "Allow complex alleles with contiguous embedded matches of up to this length.",
          "input" : "false",
          "output" : "false",
          "resource" : "false",
          "required" : "false",
          "dependent" : "false",
          "type" : "integer"
        },
        "--region" : {
          "short form argument" : "-r",
          "description" : "<chrom>:<start_position>..<end_position>. Limit analysis to the specified region, 0-base coordinates, end_position not included (same as BED format).",
          "input" : "false",
          "output" : "false",
          "resource" : "false",
          "required" : "false",
          "dependent" : "false",
          "type" : "string"
        },
        "--min-alternate-count" : {
          "short form argument" : "-C",
          "description" : "Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position.  default: 1",
          "input" : "false",
          "output" : "false",
          "resource" : "false",
          "required" : "false",
          "dependent" : "false",
          "type" : "integer"
        },
        "--min-alternate-qsum" : {
          "short form argument" : "-3",
          "description" : "Require at least this sum of quality of observation supporting an alternate allele within a single individual in order to evaluate the position.  default: 0",
          "input" : "false",
          "output" : "false",
          "resource" : "false",
          "required" : "false",
          "dependent" : "false",<commit_msg>Added --targets/-t option to freebayes config file.<commit_after>{
  "tools" : {
    "freebayes" : {
      "description" : "Bayesian variant and haplotype calling",
      "path" : "freebayes/bin",
      "executable" : "freebayes",
      "help" : "--help|-h",
      "arguments" : {
        "--bam" : {
          "short form argument" : "-b",
          "description" : "Add FILE to the set of BAM files to be analyzed.",
          "input" : "true",
          "use for filenames" : "true",
          "output" : "false",
          "resource" : "false",
          "required" : "true",
          "dependent" : "true",
          "extension" : "bam",
          "if input is stream" : "replace",
          "replace argument with" : {
            "argument" : "--stdin",
            "value" : "no value"
          },
          "type" : "string",
          "allow multiple definitions" : "true"
        },
        "--bam-list" : {
          "short form argument" : "-bl",
          "description" : "the input BAM file list.",
          "input" : "true",
          "output" : "false",
          "required" : "false",
          "resource" : "false",
          "dependent" : "true",
          "type" : "string",
          "extension" : "bam",
          "list of input files" : "true",
          "apply by repeating this argument" : "--bam"
        },
        "--vcf" : {
          "short form argument" : "-v",
          "description" : "Output VCF-format results to FILE.",
          "input" : "false",
          "output" : "true",
          "resource" : "false",
          "required" : "true",
          "dependent" : "false",
          "extension" : "vcf",
          "type" : "string",
          "if output to stream" : "do not include"
        },
        "--fasta-reference" : {
          "short form argument" : "-f",
          "description" : "Use FILE as the reference sequence for analysis.",
          "input" : "true",
          "output" : "false",
          "resource" : "true",
          "required" : "true",
          "dependent" : "true",
          "extension" : "fa|fasta",
          "type" : "string"
        },
        "--no-snps" : {
          "short form argument" : "-I",
          "description" : "Ignore SNP alleles.",
          "input" : "false",
          "output" : "false",
          "resource" : "false",
          "required" : "false",
          "dependent" : "false",
          "type" : "flag"
        },
        "--no-indels" : {
          "short form argument" : "-i",
          "description" : "Ignore insertion and deletion alleles.",
          "input" : "false",
          "output" : "false",
          "resource" : "false",
          "required" : "false",
          "dependent" : "false",
          "type" : "flag"
        },
        "--no-mnps" : {
          "short form argument" : "-X",
          "description" : "Ignore multi-nuceotide polymorphisms, MNPs.",
          "input" : "false",
          "output" : "false",
          "resource" : "false",
          "required" : "false",
          "dependent" : "false",
          "type" : "flag"
        },
        "--no-complex" : {
          "short form argument" : "-u",
          "description" : "Ignore complex events (composites of other classes).",
          "input" : "false",
          "output" : "false",
          "resource" : "false",
          "required" : "false",
          "dependent" : "false",
          "type" : "flag"
        },
        "--use-best-n-alleles" : {
          "short form argument" : "-n",
          "description" : "Evaluate only the best N SNP alleles, ranked by sum of supporting quality scores.  (Set to 0 to use all; default: all)",
          "input" : "false",
          "output" : "false",
          "resource" : "false",
          "required" : "false",
          "dependent" : "false",
          "type" : "integer"
        },
        "--max-complex-gap" : {
          "short form argument" : "-E",
          "description" : "Allow complex alleles with contiguous embedded matches of up to this length.",
          "input" : "false",
          "output" : "false",
          "resource" : "false",
          "required" : "false",
          "dependent" : "false",
          "type" : "integer"
        },
        "--region" : {
          "short form argument" : "-r",
          "description" : "<chrom>:<start_position>..<end_position>. Limit analysis to the specified region, 0-base coordinates, end_position not included (same as BED format).",
          "input" : "false",
          "output" : "false",
          "resource" : "false",
          "required" : "false",
          "dependent" : "false",
          "type" : "string"
        },
        "--targets" : {
          "short form argument" : "-t",
          "description" : "<FILE>. Limit analysis to targets listed in the BED-format FILE.",
          "input" : "true",
          "output" : "false",
          "resource" : "false",
          "required" : "false",
          "dependent" : "true",
          "extension" : "bed",
          "type" : "string"
        },
        "--min-alternate-count" : {
          "short form argument" : "-C",
          "description" : "Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position.  default: 1",
          "input" : "false",
          "output" : "false",
          "resource" : "false",
          "required" : "false",
          "dependent" : "false",
          "type" : "integer"
        },
        "--min-alternate-qsum" : {
          "short form argument" : "-3",
          "description" : "Require at least this sum of quality of observation supporting an alternate allele within a single individual in order to evaluate the position.  default: 0",
          "input" : "false",
          "output" : "false",
          "resource" : "false",
          "required" : "false",
          "dependent" : "false",
{'fraction_non_alphanumeric': 0.16511341656409353, 'fraction_numerical': 0.0008791981712678037, 'mean_word_length': 1.6053595968850207, 'pattern_counts': {'":': 0, '<': 10, '<?xml version=': 0, '>': 10, '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': '2115803', 'n_tokens_mistral': 3255, 'n_tokens_neox': 3183, 'n_words': 917}