LICENSE
README.md
pyproject.toml
src/getRPF/__init__.py
src/getRPF/cli.py
src/getRPF/architectures/__init__.py
src/getRPF/architectures/arabidopsis_thaliana_timeseries.yaml
src/getRPF/architectures/comprehensive_adapter_check.yaml
src/getRPF/architectures/ena_riboseq_standard.yaml
src/getRPF/architectures/err605046_stau1_riboseq.yaml
src/getRPF/architectures/generic_umi_protocol.yaml
src/getRPF/architectures/ingolia_2009.yaml
src/getRPF/architectures/mcglincy_ingolia_2017.yaml
src/getRPF/architectures/observed_atgtacac_3p_adapter.yaml
src/getRPF/architectures/observed_ctgtaggc_3p_adapter.yaml
src/getRPF/architectures/observed_ctgtaggc_variant_3p_adapter.yaml
src/getRPF/architectures/observed_dual_ligation_adapter_pair.yaml
src/getRPF/architectures/observed_ingolia_variant_atct_adapter.yaml
src/getRPF/architectures/observed_nextera_template_switch_6n_adapter.yaml
src/getRPF/architectures/observed_polya_a10_tail.yaml
src/getRPF/architectures/observed_protocols_README.md
src/getRPF/architectures/observed_small_rna_composite_3p_adapter.yaml
src/getRPF/architectures/observed_small_rna_tgga18_adapter.yaml
src/getRPF/architectures/observed_small_rna_truseq_composite_adapter.yaml
src/getRPF/architectures/observed_truseq_18nt_3p_adapter.yaml
src/getRPF/architectures/observed_truseq_21nt_3p_adapter.yaml
src/getRPF/architectures/observed_truseq_26nt_3p_adapter.yaml
src/getRPF/architectures/observed_truseq_core_tcgt_adapter.yaml
src/getRPF/architectures/observed_truseq_full_34nt_3p_adapter.yaml
src/getRPF/architectures/observed_truseq_prefixed_aagat_adapter.yaml
src/getRPF/architectures/observed_truseq_short_agatcggag_adapter.yaml
src/getRPF/architectures/observed_truseq_variant_atcgtatgcc_adapter.yaml
src/getRPF/architectures/preprocessed_with_adapter_contamination.yaml
src/getRPF/architectures/riboflow_template_switch.yaml
src/getRPF/architectures/tcp_seq_se100.yaml
src/getRPF/core/__init__.py
src/getRPF/core/apply.py
src/getRPF/core/checkers.py
src/getRPF/core/handlers.py
src/getRPF/core/pipeline.py
src/getRPF/core/release.py
src/getRPF/core/samplesheet.py
src/getRPF/core/seqspec_generator.py
src/getRPF/core/seqspec_loader.py
src/getRPF/core/processors/__init__.py
src/getRPF/core/processors/adapter.py
src/getRPF/core/processors/alignment.py
src/getRPF/core/processors/alignment_extractor.py
src/getRPF/core/processors/boundary.py
src/getRPF/core/processors/check.py
src/getRPF/core/processors/collapsed.py
src/getRPF/core/processors/consensus.py
src/getRPF/core/processors/identity_screen.py
src/getRPF/core/processors/matcher.py
src/getRPF/core/processors/reporting.py
src/getRPF/core/processors/rpf_extractor.py
src/getRPF/core/processors/segmenter.py
src/getRPF/core/processors/signals.py
src/getRPF/core/processors/sketch.py
src/getRPF/core/processors/types.py
src/getRPF/core/structure/__init__.py
src/getRPF/core/structure/align.py
src/getRPF/core/structure/anchors.py
src/getRPF/core/structure/assemble.py
src/getRPF/core/structure/benchmark.py
src/getRPF/core/structure/config.py
src/getRPF/core/structure/model.py
src/getRPF/core/structure/observe.py
src/getRPF/core/structure/pileup.py
src/getRPF/core/structure/report.py
src/getRPF/core/structure/seqspec_io.py
src/getRPF/core/structure/transform.py
src/getRPF/core/structure/workflow.py
src/getRPF/duckdb/ingest.py
src/getRPF/utils/__init__.py
src/getRPF/utils/file_utils.py
src/getRPF/utils/logging.py
src/getRPF/utils/validation.py
src/getRPF/viz/__init__.py
src/getRPF/viz/hmm_plot.py
src/getRPF/viz/softclip_plot.py
src/getrpf.egg-info/PKG-INFO
src/getrpf.egg-info/SOURCES.txt
src/getrpf.egg-info/dependency_links.txt
src/getrpf.egg-info/entry_points.txt
src/getrpf.egg-info/requires.txt
src/getrpf.egg-info/top_level.txt
tests/test_cli.py