LICENSE
README.md
setup.py
str_analysis/__init__.py
str_analysis/add_adjacent_loci_to_expansion_hunter_catalog.py
str_analysis/add_adjacent_loci_to_expansion_hunter_catalog__manual_unittest.py
str_analysis/add_offtarget_regions.py
str_analysis/annotate_EHdn_locus_outliers.py
str_analysis/annotate_and_filter_str_catalog.py
str_analysis/call_non_ref_motifs.py
str_analysis/check_combined_non_ref_pathogenic_motifs.py
str_analysis/check_combined_results_tsv_for_genome_wide_repeats.py
str_analysis/check_combined_results_tsv_for_pathogenic_repeats.py
str_analysis/check_trios_for_mendelian_violations.py
str_analysis/check_trios_for_mendelian_violations_tests.py
str_analysis/combine_json_to_tsv.py
str_analysis/combine_str_json_to_tsv.py
str_analysis/combine_str_json_to_tsv_tests.py
str_analysis/compute_catalog_stats.py
str_analysis/convert_annotated_EHdn_locus_outliers_to_expansion_hunter_catalog.py
str_analysis/convert_bed_to_expansion_hunter_variant_catalog.py
str_analysis/convert_dat_to_bed.py
str_analysis/convert_expansion_hunter_denovo_locus_tsv_to_bed.py
str_analysis/convert_expansion_hunter_variant_catalog_to_gangstr_spec.py
str_analysis/convert_expansion_hunter_variant_catalog_to_hipstr_format.py
str_analysis/convert_expansion_hunter_variant_catalog_to_longtr_format.py
str_analysis/convert_expansion_hunter_variant_catalog_to_trgt_catalog.py
str_analysis/convert_gangstr_spec_to_expansion_hunter_variant_catalog.py
str_analysis/convert_gangstr_vcf_to_expansion_hunter_json.py
str_analysis/convert_hipstr_vcf_to_expansion_hunter_json.py
str_analysis/convert_strling_calls_to_expansion_hunter_json.py
str_analysis/convert_trgt_vcf_to_expansion_hunter_json.py
str_analysis/copy_EH_vcf_fields_to_json.py
str_analysis/filter_vcf_to_STR_variants.py
str_analysis/filter_vcf_to_STR_variants_tests.py
str_analysis/generate_gnomad_json.py
str_analysis/generate_gnomad_json_tests.py
str_analysis/gnomad_sample_qc.py
str_analysis/make_bamlet.py
str_analysis/make_bamlet_original.py
str_analysis/make_cramlet_from_cram_in_google_storage.py
str_analysis/make_minicram.py
str_analysis/merge_loci.py
str_analysis/print_reads.py
str_analysis/run_reviewer.py
str_analysis/simulate_str_expansions.py
str_analysis/simulate_str_expansions_tests.py
str_analysis/trim_repeat_loci.py
str_analysis.egg-info/PKG-INFO
str_analysis.egg-info/SOURCES.txt
str_analysis.egg-info/dependency_links.txt
str_analysis.egg-info/entry_points.txt
str_analysis.egg-info/requires.txt
str_analysis.egg-info/top_level.txt
str_analysis/data/non_ref_motif.locus_info.json
str_analysis/data/non_ref_motif.offtarget_regions.json.gz
str_analysis/data/tests/FXN.wgsim_HET_250xGAA.bam
str_analysis/data/tests/FXN.wgsim_HET_250xGAA.bam.bai
str_analysis/data/tests/FXN.wgsim_HET_250xGAA.cram
str_analysis/data/tests/FXN.wgsim_HET_250xGAA.cram.crai
str_analysis/data/tests/__init__.py
str_analysis/utils/__init__.py
str_analysis/utils/bam_utils.py
str_analysis/utils/canonical_repeat_unit.py
str_analysis/utils/canonical_repeat_unit_tests.py
str_analysis/utils/cram_bam_utils.py
str_analysis/utils/cram_bam_utils_tests.py
str_analysis/utils/dat_utils.py
str_analysis/utils/eh_catalog_utils.py
str_analysis/utils/eh_catalog_utils_tests.py
str_analysis/utils/ehdn_info_for_locus.py
str_analysis/utils/export_json.py
str_analysis/utils/fasta_utils.py
str_analysis/utils/file_utils.py
str_analysis/utils/find_repeat_unit.py
str_analysis/utils/find_repeat_unit_tests.py
str_analysis/utils/get_adjacent_repeats.py
str_analysis/utils/gtf_utils.py
str_analysis/utils/gtf_utils__manual_unittest.py
str_analysis/utils/known_pathogenic_strs_tsv.py
str_analysis/utils/misc_utils.py
str_analysis/utils/most_frequent_repeat_unit.py
str_analysis/utils/most_frequent_repeat_unit_tests.py
str_analysis/utils/strling_info_for_locus.py
str_analysis/utils/trf_runner.py