Dockerfile
LICENSE
MANIFEST.in
README.md
manual.pdf
setup.py
seq_tools.egg-info/PKG-INFO
seq_tools.egg-info/SOURCES.txt
seq_tools.egg-info/dependency_links.txt
seq_tools.egg-info/entry_points.txt
seq_tools.egg-info/top_level.txt
seqtools/__init__.py
seqtools/align.py
seqtools/basics.py
seqtools/errors.py
seqtools/old_graph.py
seqtools/quantification.py
seqtools/stream.py
seqtools/cli/__init__.py
seqtools/cli/cli_front.py
seqtools/cli/legacy/IDP_merge_genepred.py
seqtools/cli/legacy/add_UCSC_URL_to_bed.py
seqtools/cli/legacy/annotate_psl_with_gpd.py
seqtools/cli/legacy/background.py
seqtools/cli/legacy/background_and_nascent_expression.py
seqtools/cli/legacy/bam_sort_list.py
seqtools/cli/legacy/bam_to_bed_depth_fast.py
seqtools/cli/legacy/bam_to_bed_exons.py
seqtools/cli/legacy/bam_to_best_bam.py
seqtools/cli/legacy/bam_to_downsampled_bam.py
seqtools/cli/legacy/bam_to_genepred.py
seqtools/cli/legacy/bam_to_longest_pacbio_molecule_bam.py
seqtools/cli/legacy/bam_to_ont_best_molecule_bam.py
seqtools/cli/legacy/bam_to_read_count.py
seqtools/cli/legacy/bam_to_vcf.py
seqtools/cli/legacy/bed_depth_to_bias_table.py
seqtools/cli/legacy/bed_depth_to_stratified_percentage_bed.py
seqtools/cli/legacy/bed_tools.py
seqtools/cli/legacy/bestannotation_into_rarefraction.py
seqtools/cli/legacy/bio_to_lengths.py
seqtools/cli/legacy/bwa_sam_to_gpd.py
seqtools/cli/legacy/cat_numerical.py
seqtools/cli/legacy/change_UCSC_bed_color.py
seqtools/cli/legacy/combine_bam.py
seqtools/cli/legacy/combine_splicemap_junction_color_bed.py
seqtools/cli/legacy/consecutive_junction_true_negative_detector.py
seqtools/cli/legacy/convert_BWA-mem_to_psl.py
seqtools/cli/legacy/defragment_PSL_alignments.py
seqtools/cli/legacy/du_threaded.py
seqtools/cli/legacy/explode_bam.py
seqtools/cli/legacy/explode_fastq.py
seqtools/cli/legacy/extract_ont_fastq.py
seqtools/cli/legacy/fasta_to_average_read_size.py
seqtools/cli/legacy/fastq_bgzf_index.py
seqtools/cli/legacy/fastq_quality_profiler.py
seqtools/cli/legacy/fastq_to_unmapped_sam.py
seqtools/cli/legacy/filter_psl.py
seqtools/cli/legacy/filter_sam_by_name_list.py
seqtools/cli/legacy/filter_sam_junctions.py
seqtools/cli/legacy/filter_sam_positional_duplicates.py
seqtools/cli/legacy/filter_vcf.py
seqtools/cli/legacy/filtered_gene_list_from_cufflinks_results.py
seqtools/cli/legacy/find_equivalent_splice_coordinates.py
seqtools/cli/legacy/find_novel_regions_per_read_depth.py
seqtools/cli/legacy/find_primers.py
seqtools/cli/legacy/fix_psl_stats.py
seqtools/cli/legacy/genepred_intersect.py
seqtools/cli/legacy/genepred_to_ARS_transcriptome_fasta.py
seqtools/cli/legacy/genepred_to_alignment_lengths.py
seqtools/cli/legacy/genepred_to_exon_bed.py
seqtools/cli/legacy/genepred_to_fake_psl.py
seqtools/cli/legacy/genepred_to_loci.py
seqtools/cli/legacy/get_chromosome_names_from_fasta.py
seqtools/cli/legacy/get_compatible_gpds.py
seqtools/cli/legacy/get_md5sum_on_all_files_in_directory.py
seqtools/cli/legacy/get_meta_data_from_PSL_alignments.py
seqtools/cli/legacy/get_overlap_bias_by_depth.py
seqtools/cli/legacy/get_psl_quality.py
seqtools/cli/legacy/gff3_to_genepred.py
seqtools/cli/legacy/gmap_to_bam.py
seqtools/cli/legacy/gmap_to_psl.py
seqtools/cli/legacy/gpd_intersect_bed_depth.py
seqtools/cli/legacy/gpd_to_bam_read_coverage.py
seqtools/cli/legacy/gpd_to_gc_bias.py
seqtools/cli/legacy/gpd_to_nonredundant.old.py
seqtools/cli/legacy/gpd_to_nonredundant.py
seqtools/cli/legacy/gpd_to_read_coverage.py
seqtools/cli/legacy/gpd_to_slr.py
seqtools/cli/legacy/hisat_to_mapping_count.py
seqtools/cli/legacy/hisat_to_uniquely_mapped.py
seqtools/cli/legacy/idp_gene_identification_rate.py
seqtools/cli/legacy/idp_output_to_bed_depth.py
seqtools/cli/legacy/junction_fix.py
seqtools/cli/legacy/list_bam_read_counts.py
seqtools/cli/legacy/make_unique_genepred.py
seqtools/cli/legacy/map_long_reads.py
seqtools/cli/legacy/nudge_psl_junctions_to_reference_output_gpd.py
seqtools/cli/legacy/optimize_qc.py
seqtools/cli/legacy/pacbio_concatonate_ccs_and_longest_subreads.py
seqtools/cli/legacy/pacbio_make_ccs90-95_sub75_set.py
seqtools/cli/legacy/print_psl_alignment.py
seqtools/cli/legacy/psl_to_annotation_report.py
seqtools/cli/legacy/psl_to_best_path.py
seqtools/cli/legacy/psl_to_best_psl_entries.py
seqtools/cli/legacy/psl_to_sam.py
seqtools/cli/legacy/psl_to_target_bed.py
seqtools/cli/legacy/psl_to_target_genepred.py
seqtools/cli/legacy/rename_genepred.py
seqtools/cli/legacy/rename_to_pacbio.py
seqtools/cli/legacy/replace_LSC_corrected_with_full_when_similar_length.py
seqtools/cli/legacy/run_alignqc.py
seqtools/cli/legacy/sam_flag_filter.py
seqtools/cli/legacy/sam_mapped_count.py
seqtools/cli/legacy/sam_to_average_insert_size.py
seqtools/cli/legacy/sam_to_bed_depth.py
seqtools/cli/legacy/sam_to_best_match_count.py
seqtools/cli/legacy/sam_to_best_sam.py
seqtools/cli/legacy/sam_to_loci.py
seqtools/cli/legacy/sam_to_psl-old.py
seqtools/cli/legacy/simulate_biallelic_transcriptome.py
seqtools/cli/legacy/simulate_fusion_genome.py
seqtools/cli/legacy/simulate_transcriptome.py
seqtools/cli/legacy/smithwaterman.py
seqtools/cli/legacy/smithwatermanNT.py
seqtools/cli/legacy/smooth_genepred.py
seqtools/cli/legacy/sort.py
seqtools/cli/legacy/sort_bam.py
seqtools/cli/legacy/sort_fasta.py
seqtools/cli/legacy/sort_fastq.py
seqtools/cli/legacy/sort_genepred.py
seqtools/cli/legacy/sort_psl.py
seqtools/cli/legacy/splicemap_wrapper.py
seqtools/cli/legacy/split_bam_by_ONT_cell.py
seqtools/cli/legacy/split_bam_by_chr.py
seqtools/cli/legacy/split_bam_by_pacbio_smrt_cell.py
seqtools/cli/legacy/squish_sam.py
seqtools/cli/legacy/stat_mean.py
seqtools/cli/legacy/stat_median.py
seqtools/cli/legacy/stat_standard_deviation.py
seqtools/cli/legacy/stitch_mate_pair_alignments.py
seqtools/cli/legacy/stitch_partial_alignments.py
seqtools/cli/legacy/stringtie_gtf_to_bed_depth.py
seqtools/cli/legacy/stringtie_gtf_to_expression.py
seqtools/cli/legacy/transcriptome_psl_to_best_alignment_bed.py
seqtools/cli/legacy/transpose_matrix.py
seqtools/cli/legacy/validate_psl.py
seqtools/cli/legacy/vcf_to_biallelic_genomes.py
seqtools/cli/utilities/__init__.py
seqtools/cli/utilities/bam_bgzf_index.py
seqtools/cli/utilities/bam_to_bed_depth.py
seqtools/cli/utilities/bed_depth_to_stratified_coverage.py
seqtools/cli/utilities/bgzf.py
seqtools/cli/utilities/fasta_to_fake_fastq.py
seqtools/cli/utilities/fasta_to_tsv.py
seqtools/cli/utilities/fastq_to_fasta.py
seqtools/cli/utilities/fastq_to_salmon_quant.py
seqtools/cli/utilities/fastq_to_tsv.py
seqtools/cli/utilities/gpd_annotate.py
seqtools/cli/utilities/gpd_filter.py
seqtools/cli/utilities/gpd_reannotate.py
seqtools/cli/utilities/gpd_rename.py
seqtools/cli/utilities/gpd_to_UCSC_bed12.py
seqtools/cli/utilities/gpd_to_bed_depth.py
seqtools/cli/utilities/gpd_to_fasta.py
seqtools/cli/utilities/gpd_to_gtf_exons.py
seqtools/cli/utilities/gpd_to_nonredundant.py
seqtools/cli/utilities/gtf_to_gpd.py
seqtools/cli/utilities/iterate_salmon.py
seqtools/cli/utilities/lr_to_transcriptome.py
seqtools/cli/utilities/pacbio_best_molecule_alignments.py
seqtools/cli/utilities/sam_to_gpd.py
seqtools/cli/utilities/sam_to_psl.py
seqtools/cli/utilities/sam_to_splicemap_junction_bed.py
seqtools/cli/utilities/sam_to_splicemap_like_sam.py
seqtools/cli/utilities/simulate_tx.py
seqtools/cli/utilities/sort.py
seqtools/cli/utilities/trim_fasta.py
seqtools/cli/utilities/trim_fastq.py
seqtools/cli/utilities/tsv_to_fasta.py
seqtools/cli/utilities/tsv_to_fastq.py
seqtools/format/__init__.py
seqtools/format/bed.py
seqtools/format/bgzf.py
seqtools/format/fastq.py
seqtools/format/gpd.py
seqtools/format/gtf.py
seqtools/format/pacbio.py
seqtools/format/psl.py
seqtools/format/fasta/__init__.py
seqtools/format/fasta/test.py
seqtools/format/sam/__init__.py
seqtools/format/sam/header.py
seqtools/format/sam/test.py
seqtools/format/sam/bam/__init__.py
seqtools/format/sam/bam/bamindex.py
seqtools/format/sam/bam/files.py
seqtools/graph/__init__.py
seqtools/range/__init__.py
seqtools/range/locus.py
seqtools/range/multi.py
seqtools/sequence/__init__.py
seqtools/sequence/twobit.py
seqtools/simulation/__init__.py
seqtools/simulation/emitter.py
seqtools/simulation/permute.py
seqtools/simulation/randomsource.py
seqtools/simulation/test.py
seqtools/statistics/__init__.py
seqtools/statistics/test.py
seqtools/structure/__init__.py
seqtools/structure/gene.py
seqtools/structure/test.py
seqtools/structure/transcript/__init__.py
seqtools/structure/transcript/converters.py
seqtools/structure/transcript/group.py
seqtools/structure/transcriptome/__init__.py
seqtools/structure/transcriptome/test.py