example.diff.json

{
    "groups": [
        {
            "shared_labels": {
                "__comment__": [
                    "These are shared by all experiments in this group.",
                    "These labels are only considered after unitigs are constructed",
                    "from the experiment-specific labels specified below.",
                ],
                "in": [],
                "out": []
            },
            "experiments": [
                {
                    "__comment__": [
                        "This is an example of the k-mer-based mode.",
                        "A k-mer is an in-k-mer if it has at least in_min_fraction",
                        "(default value 1.0) in-labels.",
                        "A k-mer is an out-k-mer if it has more than out_max_fraction",
                        "(default value 0.0) out-labels.",
                    ],
                    "name": "metasub_by_kmer",
                    "in_min_fraction": 1.0,
                    "out_max_fraction": 0.1,
                    "in": ["kl_sample", "zh_sample"],
                    "out": []
                },
                {
                    "__comment__": [
                        "This is an example of the unitig-based mode.",
                        "A unitig is kept if at least unitig_in_min_fraction of its",
                        "k-mers are in-k-mers and at most unitig_out_max_fraction of",
                        "its k-mers are out-k-mers.",
                        "Also, at most unitig_other_max_fraction of its k-mers can",
                        "have other labels."
                    ],
                    "name": "metasub_other",
                    "in_min_fraction": 1.0,
                    "out_max_fraction": 0.1,
                    "unitig_in_min_fraction": 1.0,
                    "unitig_out_max_fraction": 0.1,
                    "unitig_other_max_fraction": 1.0,
                    "in": ["kl_sample", "zh_sample"],
                    "out": []
                },
                {
                    "__comment__": [
                        "e.g., find the symmetric difference of these two samples",
                        "i.e., present in one or the other, but not both"
                    ],
                    "name": "metasub_sym_diff",
                    "in_min_fraction": 0.0,
                    "out_max_fraction": 0.99,
                    "in": ["kl_sample", "zh_sample"],
                    "out": ["kl_sample", "zh_sample"]
                }
            ]
        },
        {
            "shared_labels": {
                "in": ["kl_sample"],
                "out": []
            },
            "experiments": [
                {
                    "name": "metasub_no_other",
                    "in_min_fraction": 1.0,
                    "out_max_fraction": 0.1,
                    "unitig_in_min_fraction": 1.0,
                    "unitig_out_max_fraction": 0.1,
                    "unitig_other_max_fraction": 0.0,
                    "in": ["zh_sample"]
                }
            ]
        }
    ]
}