├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── feature_request.md │ └── support_request.md └── workflows │ ├── python-publish-test.yml │ ├── python-publish.yml │ └── tests.yml ├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.rst ├── doc ├── API.rst ├── INSTALL.rst ├── Makefile ├── QUICK_START.md ├── Single_cell_tutorial.md ├── cell_barcode_count_density.png ├── cell_barcode_counts.png ├── cell_barcode_knee.png ├── common_options.rst ├── conf.py ├── faq.md ├── index.rst ├── read_start_calculation.png ├── read_start_calculation.svg ├── read_start_calculatoi.excalidraw ├── reference │ ├── count.rst │ ├── count_tab.rst │ ├── dedup.rst │ ├── extract.rst │ ├── group.rst │ └── whitelist.rst ├── regex.md ├── release_notes.rst ├── requirements.txt └── the_methods.rst ├── ez_setup.py ├── requirements.txt ├── setup.cfg ├── setup.py ├── step1_unit_test.py ├── tests ├── README ├── chr19.bam ├── chr19.bam.bai ├── chr19_gene_assigned.tsv ├── chr19_gene_assigned_cell.tsv ├── chr19_gene_tags.bam ├── chr19_gene_tags.bam.bai ├── chr19_sep.bam ├── chr19_sep.bam.bai ├── chr19_tag.bam ├── chr19_tag.bam.bai ├── chr19_tag_missing.bam ├── chr19_tag_missing.bam.bai ├── count_help ├── count_single_cells_gene_tag.tsv ├── count_single_cells_gene_tag_wide.tsv ├── count_single_gene_tag.tsv ├── count_tab.tsv ├── count_tab_cell.tsv ├── count_tab_help ├── dedup_help ├── dedup_help.txt ├── either_read.fastq.1.gz ├── either_read.fastq.2.gz ├── either_read_out.1.fastq ├── either_read_out.2.fastq ├── extract_help ├── extract_quality.fastq ├── group_adj_py3.sam ├── group_adj_py3.tsv ├── group_cluster_py3.sam ├── group_cluster_py3.tsv ├── group_contig_no_gene_tag.tsv ├── group_dir_per_gene_py3.sam ├── group_dir_per_gene_py3.tsv ├── group_dir_py3.sam ├── group_dir_py3.tsv ├── group_dir_subset_py3.sam ├── group_dir_subset_py3.tsv ├── group_dir_unmapped_py3.sam ├── group_dir_unmapped_py3.tsv ├── group_help ├── group_uniq_py3.sam ├── group_uniq_py3.tsv ├── group_unsorted_py3.sam ├── indrop.fastq.1.gz ├── indrop.fastq.2.gz ├── indrop_blacklist.tsv ├── indrop_extract_blacklist.fastq ├── indrop_extract_fuzzy.fastq ├── indrop_extract_fuzzy_filtered_out.fastq ├── indrop_fuzzy_filtered.1.fastq.gz ├── indrop_fuzzy_filtered.2.fastq.gz ├── indrop_fuzzy_whitelist.tsv ├── indrop_whitelist.tsv ├── indrop_whitelist_3_errors.tsv ├── indrop_whitelist_density.tsv ├── indrop_whitelist_ed_above_thres_corr.tsv ├── indrop_whitelist_ed_above_thres_disc.tsv ├── indrop_whitelist_filtered.fastq.1.gz ├── indrop_whitelist_no_select.tsv ├── indrop_whitelist_user.tsv ├── indrop_whitelist_user_density.tsv ├── paired.bam ├── paired.bam.bai ├── paired_group_discard_chimeras.sam ├── paired_group_discard_unmapped.sam ├── paired_group_output_chimeras.sam ├── paired_group_output_unmapped.sam ├── paired_group_use_chimeras.sam ├── paired_group_use_unmapped.sam ├── paired_ignore_tlen_tag.sam ├── processed_3prime.fastq ├── processed_single.fastq ├── read2_only_string.1.fastq ├── read2_only_string.2.fastq ├── scrb_extract.fastq ├── scrb_extract_old_style_output.fastq ├── scrb_filtered_fastq.1.gz ├── scrb_seq_barcodes ├── scrb_seq_fastq.1.gz ├── scrb_seq_fastq.2.gz ├── scrb_seq_fastq_old_style.1.gz ├── scrb_seq_fastq_old_style.2.gz ├── scrb_whitelist.tsv ├── single_adj_py3.sam ├── single_chrom_py3.sam ├── single_cluster_py3.sam ├── single_dir_2_py3.sam ├── single_dir_py3.sam ├── single_gene_tag_py3.sam ├── single_ignore_py3.sam ├── single_perc_py3.sam ├── single_sep_py3.sam ├── single_stats_py3_edit_distance.tsv ├── single_stats_py3_per_umi.tsv ├── single_stats_py3_per_umi_per_position.tsv ├── single_subset_py3.sam ├── single_tag_missing_py3.sam ├── single_tag_py3.sam ├── single_unique_py3.sam ├── slim.fastq.gz ├── test_style.py ├── test_umi_tools.py ├── tests.yaml ├── umi_tools_help ├── umi_whitelist.tsv ├── unmapped.bam ├── unmapped.bam.bai ├── whitelist_help ├── whitelist_umi_input.bam ├── whitelist_umi_input.bam.bai └── whitelist_umi_output.sam └── umi_tools 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