├── .gitignore ├── .travis.yml ├── LICENSE ├── README.md ├── archived ├── currCommand ├── edgetree.py ├── genetree.py ├── plot_talon.R ├── qtests │ ├── test_search_for_prefix.py │ └── test_search_for_suffix.py ├── sam_transcript.py ├── talon.py ├── talon_3.0down_testing_suite │ ├── Makefile │ ├── README.md │ ├── conftest.py │ ├── input_files │ │ ├── KRT17_test_case │ │ │ ├── KRT17-001.sam │ │ │ ├── KRT17.gtf │ │ │ ├── README.md │ │ │ ├── trial1_config.csv │ │ │ └── trial2_config.csv │ │ ├── gtf_database_test │ │ │ ├── README.md │ │ │ └── test.gtf │ │ ├── known_and_novel_test_case │ │ │ ├── README.md │ │ │ ├── config.csv │ │ │ ├── config2.csv │ │ │ ├── known_and_novel_test_case.gtf │ │ │ ├── known_novel_test_case.sam │ │ │ └── novel_test_case.sam │ │ └── toy_transcript │ │ │ ├── README.md │ │ │ ├── config.csv │ │ │ ├── toy_ISMs.sam │ │ │ └── toy_annot.gtf │ ├── pytest.ini │ ├── test_add_exon_to_transcript.py │ ├── test_compute_alignment_coverage.py │ ├── test_compute_alignment_identity.py │ ├── test_compute_transcript_end.py │ ├── test_database_talon_integration.py │ ├── test_get_difference.py │ ├── test_get_introns.py │ ├── test_get_overlap.py │ ├── test_novelty_types.py │ └── test_transcript_get_length.py ├── test_files │ ├── GM12878_chr1_clean.sam │ ├── file_roster.md │ └── test.gtf ├── test_match_all_transcript_vertices.py ├── transcript_match_tracker.py └── vertex.py ├── diagram.png ├── example ├── README.md ├── SIRV.fa ├── SIRV_annotation.gtf ├── aligned_reads │ ├── SIRV_rep1.sam │ └── SIRV_rep2.sam └── config.csv ├── figs ├── TALON.png ├── novelty.png └── schema_5.png ├── requirements-dev.txt ├── requirements.txt ├── setup.py ├── src └── talon │ ├── __init__.py │ ├── blank.gtf │ ├── dstruct.py │ ├── edge.py │ ├── gene.py │ ├── init_refs.py │ ├── initialize_talon_database.py │ ├── length_utils.py │ ├── logger.py │ ├── post │ ├── __init__.py │ ├── ab_utils.py │ ├── call_longest_ends.py │ ├── create_GTF_abundance_from_database.py │ ├── create_GTF_from_database.py │ ├── create_abundance_file_from_database.py │ ├── create_anndata_from_database.py │ ├── filter_talon_transcripts.py │ ├── generate_talon_report.py │ ├── get_read_annotations.py │ ├── get_transcript_sjs.py │ ├── map_antisense_genes_to_sense.py │ ├── post_utils.py │ ├── r_scripts │ │ └── generate_talon_report.R │ └── summarize_datasets.py │ ├── process_sams.py │ ├── query_utils.py │ ├── reformat_gtf.py │ ├── talon.py │ ├── talon_label_reads.py │ ├── transcript.py │ └── transcript_utils.py ├── testing_suite ├── Makefile ├── README.md ├── __init__.py ├── build_test_databases.py ├── filtering │ ├── input_files │ │ ├── dset_file.txt │ │ └── example_v4.db │ ├── make_minimal_db_for_filtering.py │ ├── optparse_mock_filt.py │ ├── test_check_db_version.py │ ├── test_fetch_known.py │ ├── test_fetch_reads_in_datasets_fracA_cutoff.py │ ├── test_filter_talon_transcripts.py │ ├── test_filters.py │ ├── test_get_novelty_df.py │ └── test_parse_datasets.py ├── helper_fns.py ├── input_files │ ├── Canx_example │ │ ├── Canx.gtf │ │ ├── Canx_refseq.gtf │ │ ├── README.md │ │ ├── config.csv │ │ └── read.sam │ ├── Map2k4_example │ │ ├── Map2k4.gtf │ │ ├── README.md │ │ ├── config.csv │ │ └── read.sam │ ├── chr11_and_Tcf3 │ │ ├── BC017.sam │ │ ├── BC018.sam │ │ ├── D12.sam │ │ ├── README.md │ │ ├── chr11_and_Tcf3.gtf │ │ ├── config.csv │ │ ├── pairings.csv │ │ ├── testing_datasets.txt │ │ ├── testing_datasets2.txt │ │ └── testing_whitelist.txt │ ├── fix_gtf │ │ └── toy_annot_no_genes.gtf │ ├── intergenic_GM12878 │ │ ├── README.md │ │ ├── chr22.gtf │ │ ├── config.csv │ │ └── intergenic_GM12878.sam │ ├── longest_ends │ │ ├── test_annot.tsv │ │ └── test_gtf.gtf │ ├── monoexonic_handling │ │ ├── README.md │ │ ├── config.csv │ │ ├── monoexon.gtf │ │ └── monoexon_reads.sam │ ├── multiexon_read_overlapping_monoexon_transcript │ │ ├── HMGB1P1.gtf │ │ ├── config.csv │ │ └── read.sam │ ├── preprocess_sam │ │ ├── read1.sam │ │ └── read2.sam │ ├── readthrough │ │ ├── config.csv │ │ ├── hl60_1_1_subset_remapped_sorted.bam │ │ ├── hl60_1_1_subset_remapped_sorted.bam.bai │ │ ├── hl60_1_1_subset_remapped_sorted.sam │ │ └── readthrough.gtf │ ├── test_get_transcript_sjs_util │ │ ├── annot.gtf │ │ ├── antisense_exon.gtf │ │ ├── intron_NIC.gtf │ │ ├── intron_NNC_acceptor.gtf │ │ ├── intron_NNC_donor.gtf │ │ ├── intron_config.csv │ │ ├── intron_novel_antisense.gtf │ │ ├── known.gtf │ │ ├── test_reads.sam │ │ └── transcript_exon_assignment.gtf │ ├── test_parse_custom_SAM_tags │ │ └── toy_reads.sam │ └── toy_transcript │ │ ├── README.md │ │ ├── config.csv │ │ ├── mod_config.csv │ │ ├── toy_ISMs.sam │ │ ├── toy_annot.gtf │ │ └── toy_reads_for_partition_test.sam ├── pytest.ini ├── talon_label_reads │ ├── optparse_mock.py │ ├── test_compute_frac_As.py │ ├── test_compute_frac_as_after_transcript.py │ ├── test_compute_transcript_end.py │ ├── test_fetch_range_after_transcript.py │ ├── test_fetch_seq.py │ ├── test_inputs │ │ ├── minus_strand_read.sam │ │ ├── plus_strand_read.sam │ │ ├── pool_test │ │ │ ├── file1.sam │ │ │ ├── file1_read_labels.tsv │ │ │ ├── file2.sam │ │ │ ├── file2_read_labels.tsv │ │ │ ├── file3.sam │ │ │ └── file3_read_labels.tsv │ │ ├── test_split_by_chrom │ │ │ ├── sample_reads.bam │ │ │ └── sample_reads.sam │ │ ├── toy_genome.fa │ │ └── toy_genome.fa.fai │ ├── test_main.py │ ├── test_pool_outputs.py │ ├── test_run_chrom_thread.py │ └── test_split_reads_by_chrom.py ├── test_FSM_identification.py ├── test_ISM_identification.py ├── test_NIC_identification.py ├── test_NNC_identification.py ├── test_abundance_utility.py ├── test_all_SJs_known.py ├── test_all_exons_known.py ├── test_all_exons_novel.py ├── test_assignment_chr11_and_Tcf3_examples.py ├── test_assignment_readthrough_examples.py ├── test_compute_alignment_coverage.py ├── test_compute_alignment_identity.py ├── test_compute_delta.py ├── test_compute_exon_lengths.py ├── test_compute_jI.py ├── test_compute_transcript_end.py ├── test_compute_transcript_model_length_from_exons.py ├── test_create_temp_gene_table.py ├── test_database_updates.py ├── test_find_gene_match_on_vertex_basis.py ├── test_get_introns.py ├── test_get_overlap.py ├── test_get_transcript_sjs_util.py ├── test_identification_flow.py ├── test_longest_ends.py ├── test_make_edge_dict.py ├── test_make_gene_start_end_dict.py ├── test_make_location_dict.py ├── test_make_read_annot_file.py ├── test_make_temp_monoexonic_transcript_table.py ├── test_make_temp_novel_gene_table.py ├── test_make_transcript_dict.py ├── test_make_vertex_2_gene_dict.py ├── test_match_all_splice_edges.py ├── test_match_all_splice_vertices.py ├── test_match_all_transcript_edges.py ├── test_monoexonic.py ├── test_monoexonic_genomic_edge_case.py ├── test_multiexon_read_overlapping_monoexon_transcript.py ├── test_parse_custom_SAM_tags.py ├── test_partition_reads.py ├── test_permissive_match.py ├── test_post_talon_utils.py ├── test_preprocess_sam_dataset_labeling.py ├── 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