LICENSE.txt
README.md
pyproject.toml
setup.py
src/lhc/__init__.py
src/lhc/cli/__init__.py
src/lhc/cli/alignments/__init__.py
src/lhc/cli/alignments/__main__.py
src/lhc/cli/alignments/cs_to_table.py
src/lhc/cli/alignments/mismatch_filter.py
src/lhc/cli/alignments/strand.py
src/lhc/cli/loci/__init__.py
src/lhc/cli/loci/__main__.py
src/lhc/cli/loci/closest.py
src/lhc/cli/loci/deduplicate.py
src/lhc/cli/loci/difference.py
src/lhc/cli/loci/extend.py
src/lhc/cli/loci/filter.py
src/lhc/cli/loci/flank.py
src/lhc/cli/loci/generate.py
src/lhc/cli/loci/intersect.py
src/lhc/cli/loci/kmer_filter.py
src/lhc/cli/loci/stats.py
src/lhc/cli/loci/union.py
src/lhc/cli/loci/view.py
src/lhc/cli/multiple_alignments/__init__.py
src/lhc/cli/multiple_alignments/__main__.py
src/lhc/cli/multiple_alignments/align_pairwise.py
src/lhc/cli/multiple_alignments/call_variants.py
src/lhc/cli/multiple_alignments/extract.py
src/lhc/cli/multiple_alignments/get_consensus.py
src/lhc/cli/multiple_alignments/trim_gaps.py
src/lhc/cli/sequences/__init__.py
src/lhc/cli/sequences/__main__.py
src/lhc/cli/sequences/barcode_filter.py
src/lhc/cli/sequences/barcode_split.py
src/lhc/cli/sequences/extract.py
src/lhc/cli/sequences/filter.py
src/lhc/cli/sequences/interleave.py
src/lhc/cli/sequences/reverse_complement.py
src/lhc/cli/sequences/rmdup.py
src/lhc/cli/sequences/split.py
src/lhc/cli/sequences/stat_.py
src/lhc/cli/sequences/unique.py
src/lhc/cli/sequences/view.py
src/lhc/cli/variants/__init__.py
src/lhc/cli/variants/__main__.py
src/lhc/cli/variants/annotate.py
src/lhc/cli/variants/compare.py
src/lhc/cli/variants/diff.py
src/lhc/cli/variants/filter.py
src/lhc/cli/variants/merge.py
src/lhc/cli/variants/sample.py
src/lhc/cli/variants/shift.py
src/lhc/cli/variants/split_alt.py
src/lhc/cli/variants/trim_alt.py
src/lhc/collections/__init__.py
src/lhc/collections/interval_set.py
src/lhc/collections/one_pass_interval_set.py
src/lhc/collections/sequence_set.py
src/lhc/collections/tabix_file_wrapper.py
src/lhc/data/Emolwt.dat
src/lhc/data/gc.prt
src/lhc/entities/__init__.py
src/lhc/entities/genomic_coordinate/__init__.py
src/lhc/entities/genomic_coordinate/genomic_interval.py
src/lhc/entities/genomic_coordinate/genomic_position.py
src/lhc/entities/genomic_coordinate/nested_genomic_interval.py
src/lhc/entities/interval/__init__.py
src/lhc/entities/interval/binner.py
src/lhc/entities/interval/interval.py
src/lhc/entities/interval/set_operations.py
src/lhc/entities/locus/__init__.py
src/lhc/entities/locus/make_loci.py
src/lhc/entities/multiple_alignment/__init__.py
src/lhc/entities/multiple_alignment/aligner.py
src/lhc/entities/multiple_alignment/alignment.py
src/lhc/entities/multiple_alignment/character_map.py
src/lhc/entities/multiple_alignment/global_alignment.py
src/lhc/entities/multiple_alignment/local_alignment.py
src/lhc/entities/multiple_alignment/score.py
src/lhc/entities/multiple_alignment/semiglobal_alignment.py
src/lhc/entities/sequence/__init__.py
src/lhc/entities/sequence/dicodonshuffle.py
src/lhc/entities/sequence/reverse_complement.py
src/lhc/entities/sequence/sequence_generator.py
src/lhc/entities/variant/__init__.py
src/lhc/entities/variant/amino_acid_variant.py
src/lhc/entities/variant/coding_variant.py
src/lhc/entities/variant/codon_variant.py
src/lhc/entities/variant/merger.py
src/lhc/entities/variant/variant.py
src/lhc/entities/variant/variant_effect.py
src/lhc/graph/__init__.py
src/lhc/graph/graph.py
src/lhc/graph/hyper_graph.py
src/lhc/graph/n_partite_graph.py
src/lhc/graph/n_partite_graph_printer.py
src/lhc/io/__init__.py
src/lhc/io/cut.py
src/lhc/io/file.py
src/lhc/io/filepool.py
src/lhc/io/alignment/__init__.py
src/lhc/io/alignment/alignment.py
src/lhc/io/alignment/alignment_file.py
src/lhc/io/alignment/clustal.py
src/lhc/io/alignment/fasta.py
src/lhc/io/alignment/table.py
src/lhc/io/locus/__init__.py
src/lhc/io/locus/bed.py
src/lhc/io/locus/embl.py
src/lhc/io/locus/gbk.py
src/lhc/io/locus/gff.py
src/lhc/io/locus/gtf.py
src/lhc/io/locus/locus_file.py
src/lhc/io/locus/paf.py
src/lhc/io/locus/region.py
src/lhc/io/locus/repeat_masker.py
src/lhc/io/locus/sam.py
src/lhc/io/methpat/__init__.py
src/lhc/io/methpat/__main__.py
src/lhc/io/methpat/tools/extract_patterns.py
src/lhc/io/sequence/__init__.py
src/lhc/io/sequence/embl.py
src/lhc/io/sequence/fasta.py
src/lhc/io/sequence/fastq.py
src/lhc/io/sequence/sequence_file.py
src/lhc/io/variant/__init__.py
src/lhc/io/variant/maf.py
src/lhc/io/variant/variant_file.py
src/lhc/io/variant/vcf.py
src/lhc/itertools/__init__.py
src/lhc/itertools/chunked_iterator.py
src/lhc/itertools/merge_sorted.py
src/lhc/itertools/sorted_iterator_merger.py
src/lhc/misc/__init__.py
src/lhc/misc/argparse.py
src/lhc/misc/genetic_code.py
src/lhc/misc/iupac.py
src/lhc/misc/kmer.py
src/lhc/misc/natural_key.py
src/lhc/misc/performance_measures.py
src/lhc/misc/reservoir.py
src/lhc/misc/skew.py
src/lhc/misc/string.py
src/lhc/misc/tokeniser.py
src/lhc_python.egg-info/PKG-INFO
src/lhc_python.egg-info/SOURCES.txt
src/lhc_python.egg-info/dependency_links.txt
src/lhc_python.egg-info/requires.txt
src/lhc_python.egg-info/top_level.txt
src/lib/bitap/bitap.cpp
src/lib/bitap/bitap.h
src/lib/bitap/bitapmodule.cpp
src/lib/digen/__init__.py
src/lib/digen/digen.cpp
src/lib/digen/digen.h
src/lib/digen/digen.py
src/lib/digen/digenmodule.cpp
src/lib/digen/setup.py