.coveragerc
.git_archival.txt
.gitattributes
.gitignore
.gitlab-ci.yml
LICENSE
README.md
pyproject.toml
setup.cfg
docs/.gitkeep
docs/Makefile
docs/conf.py
docs/effect_HIW.rst
docs/effect_code.rst
docs/effect_example_data.rst
docs/effect_faq.rst
docs/effect_feature_definition.rst
docs/effect_scope_quickstart.rst
docs/index.rst
docs/index_manual.txt
docs/images/Haplotype_window.png
docs/images/SMAP_effect-prediction.png
docs/images/SMAP_global_overview_sites_window_design_effect_WGS_transparent.png
docs/images/frequency_distribution.png
docs/images/HowItWorks/Adjusted_ORF_haplotype_name_V4_translations_alignment.png
docs/images/HowItWorks/Adjusted_ORF_haplotype_name_V4_zoom_exon4_translation.png
docs/images/HowItWorks/Discretize_LOF_frequencies.png
docs/images/HowItWorks/Discretize_LOF_frequencies_all9genes_newFreq.png
docs/images/HowItWorks/HIW_align.png
docs/images/HowItWorks/HIW_collect.png
docs/images/HowItWorks/HIW_collect_ROI.png
docs/images/HowItWorks/HIW_collect_ROI_CRISPR.png
docs/images/HowItWorks/HIW_collect_ROI_CRISPR_double_guide_non-overlap.png
docs/images/HowItWorks/HIW_collect_ROI_CRISPR_double_guide_overlap.png
docs/images/HowItWorks/HIW_collect_ROI_CRISPR_double_guide_overlap_s12.png
docs/images/HowItWorks/HIW_collect_ROI_CRISPR_double_guides.png
docs/images/HowItWorks/HIW_collect_ROI_CRISPR_single_guide_forward.png
docs/images/HowItWorks/HIW_collect_ROI_CRISPR_single_guide_reverse.png
docs/images/HowItWorks/HIW_collect_ROI_Nat_Var.png
docs/images/HowItWorks/HIW_design.png
docs/images/HowItWorks/HIW_gene.png
docs/images/HowItWorks/HIW_window.png
docs/images/HowItWorks/Haplotype_window_interpretation_WT_v2.png
docs/images/HowItWorks/INDELS_gaps.png
docs/images/HowItWorks/LOF_discrete_call_table.png
docs/images/HowItWorks/ROI.png
docs/images/HowItWorks/ROI_coordinate.png
docs/images/HowItWorks/ROI_hap_a.png
docs/images/HowItWorks/ROI_hap_a_new.png
docs/images/HowItWorks/ROI_hap_a_new2.png
docs/images/HowItWorks/ROI_hap_b.png
docs/images/HowItWorks/ROI_hap_b_new.png
docs/images/HowItWorks/ROI_hap_b_new2.png
docs/images/HowItWorks/ROI_hap_c.png
docs/images/HowItWorks/ROI_hap_c_new.png
docs/images/HowItWorks/ROI_hap_c_new2.png
docs/images/HowItWorks/ROI_hap_d.png
docs/images/HowItWorks/ROI_hap_d_new.png
docs/images/HowItWorks/ROI_hap_d_new2.png
docs/images/HowItWorks/ROI_hap_e.png
docs/images/HowItWorks/ROI_hap_e_new.png
docs/images/HowItWorks/ROI_hap_e_new2.png
docs/images/HowItWorks/ROI_hap_e_new_neighbor_SNP.png
docs/images/HowItWorks/ROI_hap_f.png
docs/images/HowItWorks/ROI_hap_f_new.png
docs/images/HowItWorks/ROI_hap_f_new2.png
docs/images/HowItWorks/ROI_hap_forward.png
docs/images/HowItWorks/ROI_hap_forward_no_name.png
docs/images/HowItWorks/ROI_hap_forward_reverse.png
docs/images/HowItWorks/ROI_hap_g.png
docs/images/HowItWorks/ROI_hap_g_new.png
docs/images/HowItWorks/ROI_hap_g_new2.png
docs/images/HowItWorks/ROI_hap_h.png
docs/images/HowItWorks/ROI_hap_h_new.png
docs/images/HowItWorks/ROI_hap_h_new2.png
docs/images/HowItWorks/ROI_hap_h_new2_neighbor_SNP.png
docs/images/HowItWorks/ROI_hap_h_new_neighbor_SNP.png
docs/images/HowItWorks/ROI_hap_i.png
docs/images/HowItWorks/ROI_hap_i_new.png
docs/images/HowItWorks/ROI_hap_i_new2.png
docs/images/HowItWorks/ROI_hap_j.png
docs/images/HowItWorks/ROI_hap_j_new.png
docs/images/HowItWorks/ROI_hap_j_new2.png
docs/images/HowItWorks/ROI_hap_k_new.png
docs/images/HowItWorks/ROI_hap_k_new2.png
docs/images/HowItWorks/ROI_hap_l_new.png
docs/images/HowItWorks/ROI_hap_l_new2.png
docs/images/HowItWorks/ROI_hap_m_new.png
docs/images/HowItWorks/ROI_hap_m_new2.png
docs/images/HowItWorks/ROI_hap_n_new2.png
docs/images/HowItWorks/ROI_hap_reverse.png
docs/images/HowItWorks/ROI_hap_reverse_no_name.png
docs/images/HowItWorks/ULM_Slide1.PNG
docs/images/HowItWorks/ULM_Slide2.PNG
docs/images/HowItWorks/ULM_Slide3.PNG
docs/images/HowItWorks/align_filter2_hap_a-d.png
docs/images/HowItWorks/align_filter2_hap_e-j.png
docs/images/HowItWorks/align_hap_a.png
docs/images/HowItWorks/align_hap_b.png
docs/images/HowItWorks/align_hap_c.png
docs/images/HowItWorks/align_hap_d.png
docs/images/HowItWorks/align_hap_e.png
docs/images/HowItWorks/align_hap_f.png
docs/images/HowItWorks/align_hap_g.png
docs/images/HowItWorks/align_hap_h.png
docs/images/HowItWorks/align_hap_i.png
docs/images/HowItWorks/align_hap_j.png
docs/images/HowItWorks/align_hap_k.png
docs/images/HowItWorks/align_hap_l.png
docs/images/HowItWorks/align_hap_m.png
docs/images/HowItWorks/align_hap_n.png
docs/images/HowItWorks/align_haplotype_name.png
docs/images/HowItWorks/align_haplotype_name_new.png
docs/images/HowItWorks/align_haplotype_name_new_v2.png
docs/images/HowItWorks/borders_A01-A09_Genename.gff
docs/images/HowItWorks/borders_TR.gff
docs/images/HowItWorks/code_SNP.png
docs/images/HowItWorks/code_definition.png
docs/images/HowItWorks/code_deletion_across.png
docs/images/HowItWorks/code_deletion_exon.png
docs/images/HowItWorks/code_insertion_down.png
docs/images/HowItWorks/code_insertion_exon.png
docs/images/HowItWorks/code_insertion_intron.png
docs/images/HowItWorks/code_insertion_up.png
docs/images/HowItWorks/code_reference_definition.png
docs/images/HowItWorks/collapse.png
docs/images/HowItWorks/genome_A01-A09_Genename.fasta
docs/images/HowItWorks/genome_A01-A09_Genename_ATG_corrected.fasta
docs/images/HowItWorks/genome_TR.fasta
docs/images/HowItWorks/guides_A01-A09_Genename.gff
docs/images/HowItWorks/guides_TR.gff
docs/images/HowItWorks/haplotype_LOF_class.png
docs/images/HowItWorks/haplotype_LOF_frequency_table.png
docs/images/HowItWorks/haplotype_collapse.png
docs/images/HowItWorks/haplotype_frequency_TR.tsv
docs/images/HowItWorks/haplotype_window.png
docs/images/HowItWorks/local_gff_file_A01-A09_Genename.gff3
docs/images/HowItWorks/local_gff_file_TR.gff
docs/images/HowItWorks/mastertable_A01-A09_targets_Genename.tsv
docs/images/example_data/102.png
docs/images/example_data/Adjusted_ORF_translations_alignment.png
docs/images/example_data/Haplotype_window.png
docs/images/example_data/Haplotype_window_interpretation_A05_A09_diversity.png
docs/images/example_data/Haplotype_window_interpretation_A09_diversity.png
docs/images/example_data/Haplotype_window_interpretation_WT.png
docs/images/example_data/Haplotype_window_interpretation_WT_heterozygous.png
docs/images/example_data/Haplotype_window_interpretation_WT_v1.png
docs/images/example_data/Haplotype_window_interpretation_WT_v2.png
docs/images/example_data/Haplotype_window_interpretation_WT_v3.png
docs/images/example_data/Haplotype_window_interpretation_master_v1.png
docs/images/example_data/Haplotype_window_interpretation_normal_genome_editing.png
docs/images/example_data/SMAP_haplotype_step6.png
docs/images/example_data/Slide2.PNG
docs/images/example_data/Slide3.PNG
docs/images/example_data/Slide4.PNG
docs/images/example_data/Slide5.PNG
docs/images/example_data/Slide6.PNG
docs/images/example_data/Slide7.PNG
docs/images/example_data/Slide8.PNG
docs/images/example_data/Zm00007a00030671-1G_ORF.png
docs/images/example_data/Zm00007a00030671-2GG_ORF.png
docs/images/example_data/Zm00007a00030671.png
docs/images/example_data/Zm00007a00030671_ORF.png
docs/images/example_data/Zm00007a00030671_allele_CDS_ORF_alignment.png
docs/images/example_data/Zm00007a00030671_allele_CDS_ORF_alignment_2.png
docs/images/example_data/Zm00007a00030671_allele_CDS_ORF_alignment_3.png
docs/images/example_data/Zm00007a00030671_allele_alignment.png
docs/images/example_data/Zm00007a00030671_allele_translated_protein_alignment.png
docs/images/example_data/Zm00007a00030671_allele_translated_protein_alignment_2.png
docs/images/example_data/Zm00007a00030671_indel.png
docs/images/example_data/Zm00007a00030671_zoom.png
docs/images/example_data/aggregated.tsv
docs/images/example_data/align_haplotype_name_new.png
docs/images/example_data/align_haplotype_name_new_v2.png
docs/images/example_data/annotate.tsv
docs/images/example_data/discretized.tsv
docs/images/example_data/newplot.png
docs/images/feature_definition/Adjusted_ORF_haplotype_name_V4_full_length.png
docs/images/feature_definition/Adjusted_ORF_haplotype_name_V4_translations_alignment.png
docs/images/feature_definition/Adjusted_ORF_haplotype_name_V4_zoom_exon4.png
docs/images/feature_definition/Adjusted_ORF_haplotype_name_V4_zoom_exon4_translation.png
docs/images/feature_definition/Adjusted_ORF_haps_V4_full_length.png
docs/images/feature_definition/Adjusted_ORF_haps_V4_translations_alignment.png
docs/images/feature_definition/Adjusted_ORF_haps_V4_translations_alignment_full.png
docs/images/feature_definition/Adjusted_ORF_haps_V4_zoom_exon4.png
docs/images/feature_definition/Adjusted_ORF_haps_V4_zoom_exon4_translation.png
docs/images/feature_definition/Discretize_LOF_frequencies.png
docs/images/feature_definition/FD_project_mutation_gene_structure.png
docs/images/feature_definition/HIW_collect_ROI_CRISPR.png
docs/images/feature_definition/Haplotype_window_interpretation_WT_v4.png
docs/images/feature_definition/Haplotype_window_interpretation_WT_v4_gene1.png
docs/images/feature_definition/Haplotype_window_interpretation_WT_v4_gene2.png
docs/images/feature_definition/Haplotype_window_interpretation_WT_v4_gene359.png
docs/images/feature_definition/Haplotype_window_interpretation_WT_v4_gene6.png
docs/images/feature_definition/Haplotype_window_interpretation_WT_v4_gene678.png
docs/images/feature_definition/Haplotype_window_interpretation_WT_v4_master.png
docs/images/feature_definition/PAM_recognition_sites_various_Cas.tsv
docs/images/feature_definition/ROI_collapse_hap_a_b_c_d_e.png
docs/images/feature_definition/feature_def_haplotype_LOF_frequency_table.png
docs/images/feature_definition/feature_definition_ROI_hap_h_new.png
docs/images/feature_definition/feature_definition_collect_ROI_CRISPR.png
smap_effect_prediction/__init__.py
smap_effect_prediction/__main__.py
smap_effect_prediction/__version__.py
smap_effect_prediction/editor.py
smap_effect_prediction/logging_configuration.py
smap_effect_prediction/models.py
smap_effect_prediction/plotting.py
smap_effect_prediction/utils.py
smap_effect_prediction.egg-info/PKG-INFO
smap_effect_prediction.egg-info/SOURCES.txt
smap_effect_prediction.egg-info/dependency_links.txt
smap_effect_prediction.egg-info/entry_points.txt
smap_effect_prediction.egg-info/requires.txt
smap_effect_prediction.egg-info/top_level.txt
smap_effect_prediction/modifications/__init__.py
smap_effect_prediction/modifications/aggregate.py
smap_effect_prediction/modifications/annotate.py
smap_effect_prediction/modifications/collapse.py
smap_effect_prediction/modifications/discretize.py
smap_effect_prediction/modifications/modification.py
test/test_aggregation.py
test/test_annotation.py
test/test_collapse.py
test/test_discritization.py
test/test_editor.py
test/test_logging.py
test/test_main.py
test/test_models.py
test/test_plotting.py
test/test_utils.py
test/test_writing.py