Index B | C | D | E | F | G | I | L | M | P | R | S | T | V | W B bam2tensor.embedding module bam2tensor.functions module bam2tensor.metadata module bam2tensor.reference module C cache_file (GenomeMethylationEmbedding attribute) CACHE_FILE_SUFFIX (in module bam2tensor.embedding) check_chromosome_overlap() (in module bam2tensor.functions) compute_cpg_index_crc32() (in module bam2tensor.metadata) count_non_cpg_retained_reference() (in module bam2tensor.functions) count_non_cpg_retained_xm() (in module bam2tensor.functions) cpg_sites_dict (GenomeMethylationEmbedding attribute) D detect_aligner() (in module bam2tensor.functions) download_reference() (in module bam2tensor.reference) E embedding_to_genomic_position() (GenomeMethylationEmbedding method) expected_chromosomes (GenomeMethylationEmbedding attribute) extract_methylation_data_from_bam() (in module bam2tensor.functions) ExtractionResult (class in bam2tensor.functions) F fasta_source (GenomeMethylationEmbedding attribute) G genome_name (GenomeMethylationEmbedding attribute) GenomeMethylationEmbedding (class in bam2tensor.embedding) genomic_position_to_embedding() (GenomeMethylationEmbedding method) get_cache_dir() (in module bam2tensor.reference) get_cached_reference() (in module bam2tensor.reference) I is_em_overconversion_read() (in module bam2tensor.functions) L list_available_genomes() (in module bam2tensor.reference) load_embedding_cache() (GenomeMethylationEmbedding method) M matrix (ExtractionResult attribute), [1] module bam2tensor.embedding bam2tensor.functions bam2tensor.metadata bam2tensor.reference P parse_fasta_for_cpg_sites() (GenomeMethylationEmbedding method) R read_npz_metadata() (in module bam2tensor.metadata) read_npz_tlen() (in module bam2tensor.metadata) S save_embedding_cache() (GenomeMethylationEmbedding method) T tlen (ExtractionResult attribute), [1] total_cpg_sites (GenomeMethylationEmbedding attribute) V verbose (GenomeMethylationEmbedding attribute) W write_npz_metadata() (in module bam2tensor.metadata) write_npz_tlen() (in module bam2tensor.metadata)