├── .github └── ISSUE_TEMPLATE │ ├── add-issue-submission-guidelines.md │ └── config.yml ├── LICENSE ├── LICENSE.allhic ├── README.md ├── README_CN.md ├── conda_env ├── create_conda_env_py310.sh ├── create_conda_env_py311.sh ├── create_conda_env_py312.sh ├── environment_py310.yml ├── environment_py311.yml └── environment_py312.yml ├── haphic ├── images ├── HapHiC1.png ├── HapHiC2.png └── refsort_example.png ├── scripts ├── HapHiC_build.py ├── HapHiC_cluster.py ├── HapHiC_pipeline.py ├── HapHiC_plot.py ├── HapHiC_reassign.py ├── HapHiC_refsort.py ├── HapHiC_sort.py ├── __init__.py ├── _version.py └── allhic ├── simulation ├── add_allele_tag.py ├── allele_statistics.py ├── allelic_contig_statistics.py ├── chimeric_contig_statistics.py ├── collapsed_contig_statistics.py ├── convert_agp_to_groups.py ├── convert_agp_to_tour.py ├── convert_assembly_to_groups.py ├── convert_assembly_to_tour.py ├── convert_lachesis_ordering_to_tour.py ├── convert_lachesis_result_to_groups.py ├── correction_analysis.py ├── density_statistics.py ├── draw_tour_file.py ├── evaluate_scaffolds.py ├── extract_SVs_from_simple.py ├── extract_corrected_ctgs_from_3d_dna_assembly.py ├── extract_corrected_ctgs_from_salsa_agp.py ├── extract_corrected_ctgs_from_yahs_agp.py ├── filter_bam_from_list.py ├── filter_fastq_len.py ├── filter_orthologous_anchors.py ├── generate_truth.py ├── generic_result_statistics.py ├── get_3d_dna_break_points.py ├── get_allhic_break_points.py ├── get_discordant_HiC_links.py ├── get_haphic_break_points.py ├── get_paf_alignments.py ├── get_salsa_break_points.py ├── get_yahs_break_points.py ├── haplotype_kmers.py ├── interpret_switch_errors.py ├── link_statistics.py ├── mock_delta.py ├── mock_delta_chrs_only.py ├── mock_gfa.py ├── pbsperf.py ├── result_statistics.py ├── sample_mnd.py ├── score_statistics.py ├── shuffle_fasta.py ├── sim_chimeric_contigs.py ├── sim_collapsed_regions.py ├── sim_contigs.py ├── sim_for_reassignment.py ├── sim_group_files.py ├── sim_haplotypes.py ├── sim_switch_errors.py ├── sort_agp.py ├── split_bam.py ├── split_clm.py ├── split_fasta.py ├── split_mnd.py ├── summarize_correction.py └── validate_mock_delta.py └── utils ├── agp_to_fasta ├── combine_groups.py ├── convert_gfa_ids.py ├── fasta_count_N.py ├── fastq_length_filtering.py ├── filter_bam ├── filter_bam.py ├── find_telomeres.py ├── gfa_depth_to_bedGraph.py ├── global_chaining.py ├── groups_to_clusters.py ├── juicer ├── juicer_tools.1.9.9_jcuda.0.8.jar ├── mock_agp_file.py ├── mock_blast_file.py ├── prepare_clusters.py ├── remove_singletons.py └── reverse_bed.py /.github/ISSUE_TEMPLATE/add-issue-submission-guidelines.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zengxiaofei/HapHiC/HEAD/.github/ISSUE_TEMPLATE/add-issue-submission-guidelines.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/config.yml: 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