├── .gitignore ├── LICENSE ├── README.md ├── config ├── config.yaml └── samples.tsv ├── scripts └── R │ ├── clustering_orient_strandstate.snakemake.R │ ├── count_alignments_fastmap.snakemake.R │ ├── count_alignments_mem.snakemake.R │ ├── dev │ ├── correspondance.R │ ├── error_rate_exploration.R │ ├── grad_perp_vector.R │ ├── haploid_chromosome_scores.R │ ├── plot_merging.R │ ├── reference_evaluation_plots.R │ └── simulated_similarities.R │ ├── explode_largest_component.R │ ├── fudge_marker_counts.snakemake.R │ ├── locate_sseq_breakpoints.snakemake.R │ └── module_utils │ ├── phasing_utils.R │ └── utils.R └── workflow ├── Snakefile ├── envs ├── env_R-COS.yaml ├── env_Renv.yaml ├── env_cl.yaml ├── env_snakemake.yaml ├── env_verkko.yaml └── env_yak.yaml └── rules ├── collect_output.smk ├── sample_table.smk └── strandseq_breakpoints.smk /.gitignore: -------------------------------------------------------------------------------- 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