Index _ | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | W | X | Z _ __getitem__() (deepbiop.fq.FastqDataset method) __getstate__() (deepbiop.fq.Predict method) __iter__() (deepbiop.fq.FastqDataset method) (deepbiop.fq.FastqIterator method) __len__() (deepbiop.fq.FastqDataset method) __next__() (deepbiop.fq.FastqIterator method) __repr__() (deepbiop.fq.FastqRecord method) (deepbiop.fq.Predict method) (deepbiop.utils.GenomicInterval method) (deepbiop.utils.PslAlignment method) __setstate__() (deepbiop.fq.Predict method) B bases (deepbiop.fa.EncoderOption property) (deepbiop.fq.EncoderOption property) Bgzip (deepbiop.utils.CompressedType attribute) Bzip2 (deepbiop.utils.CompressedType attribute) C check_compressed_type() (in module deepbiop.utils) chr (deepbiop.utils.GenomicInterval property) CompressedType (class in deepbiop.utils) convert_multiple_fas_to_one_fa() (in module deepbiop.fa) convert_multiple_fqs_to_one_fq() (in module deepbiop.fq) count_chimeric_reads_for_path() (in module deepbiop.bam) count_chimeric_reads_for_paths() (in module deepbiop.bam) D deepbiop module deepbiop.bam module deepbiop.core module deepbiop.fa module deepbiop.fq module deepbiop.utils module E encode_fa_path_to_parquet() (in module deepbiop.fa) encode_fa_path_to_parquet_chunk() (in module deepbiop.fa) encode_fa_paths_to_parquet() (in module deepbiop.fa) encode_fq_path_to_parquet() (in module deepbiop.fq) encode_fq_path_to_parquet_chunk() (in module deepbiop.fq) encode_fq_paths_to_parquet() (in module deepbiop.fq) encode_qual() (in module deepbiop.fq) EncoderOption (class in deepbiop.fa) (class in deepbiop.fq) end (deepbiop.utils.GenomicInterval property) F Fasta (deepbiop.utils.SequenceFileType attribute) Fastq (deepbiop.utils.SequenceFileType attribute) fastq_to_fasta() (in module deepbiop.fq) FastqDataset (class in deepbiop.fq) FastqIterator (class in deepbiop.fq) FastqRecord (class in deepbiop.fq) from_file() (deepbiop.fq.FastqDataset static method) G generate_kmers() (in module deepbiop.core) generate_kmers_table() (in module deepbiop.core) generate_unmaped_intervals() (in module deepbiop.utils) GenomicInterval (class in deepbiop.utils) get_label_region() (in module deepbiop.fq) get_records() (deepbiop.fq.FastqDataset method) get_records_indexed() (deepbiop.fq.FastqDataset method) get_records_sequential() (deepbiop.fq.FastqDataset method) get_stats() (deepbiop.fq.FastqDataset method) Gzip (deepbiop.utils.CompressedType attribute) H header (deepbiop.fq.FastqRecord property) highlight_targets() (in module deepbiop.utils) I id (deepbiop.fa.RecordData property) (deepbiop.fq.Predict property) (deepbiop.fq.RecordData property) identity (deepbiop.utils.PslAlignment property) is_truncated (deepbiop.fq.Predict property) K kmers_to_seq() (in module deepbiop.core) L left_right_soft_clip() (in module deepbiop.bam) load_predicts_from_batch_pt() (in module deepbiop.fq) load_predicts_from_batch_pts() (in module deepbiop.fq) M majority_voting() (in module deepbiop.utils) module deepbiop deepbiop.bam deepbiop.core deepbiop.fa deepbiop.fq deepbiop.utils N normalize_seq() (in module deepbiop.core) O overlap() (deepbiop.utils.GenomicInterval method) P ParquetEncoder (class in deepbiop.fa) (class in deepbiop.fq) parse_psl_by_qname() (in module deepbiop.utils) Predict (class in deepbiop.fq) prediction (deepbiop.fq.Predict property) prediction_region() (deepbiop.fq.Predict method) PslAlignment (class in deepbiop.utils) Q qend (deepbiop.utils.PslAlignment property) qmatch (deepbiop.utils.PslAlignment property) qname (deepbiop.utils.PslAlignment property) qsize (deepbiop.utils.PslAlignment property) qstart (deepbiop.utils.PslAlignment property) qual (deepbiop.fq.Predict property) (deepbiop.fq.RecordData property) qual_array() (deepbiop.fq.Predict method) qual_offset (deepbiop.fq.EncoderOption property) quality (deepbiop.fq.FastqRecord property) R RecordData (class in deepbiop.fa) (class in deepbiop.fq) remove_intervals_and_keep_left() (in module deepbiop.utils) reverse_complement() (in module deepbiop.core) S select_record_from_fa() (in module deepbiop.fa) select_record_from_fa_by_random() (in module deepbiop.fa) select_record_from_fq() (in module deepbiop.fq) select_record_from_fq_by_random() (in module deepbiop.fq) seq (deepbiop.fa.RecordData property) (deepbiop.fq.Predict property) (deepbiop.fq.RecordData property) seq_len() (deepbiop.fq.Predict method) seq_to_kmers() (in module deepbiop.core) sequence (deepbiop.fq.FastqRecord property) SequenceFileType (class in deepbiop.utils) show_info() (deepbiop.fq.Predict method) smooth_and_select_intervals() (deepbiop.fq.Predict method) smooth_label() (deepbiop.fq.Predict method) smooth_prediction() (deepbiop.fq.Predict method) start (deepbiop.utils.GenomicInterval property) T tend (deepbiop.utils.PslAlignment property) test_predicts() (in module deepbiop.fq) threads (deepbiop.fq.EncoderOption property) tname (deepbiop.utils.PslAlignment property) tsize (deepbiop.utils.PslAlignment property) tstart (deepbiop.utils.PslAlignment property) U Uncompress (deepbiop.utils.CompressedType attribute) Unknown (deepbiop.utils.CompressedType attribute) (deepbiop.utils.SequenceFileType attribute) W write_fa() (in module deepbiop.fa) write_fa_parallel() (in module deepbiop.fa) write_fq() (in module deepbiop.fq) write_fq_parallel() (in module deepbiop.fq) X Xz (deepbiop.utils.CompressedType attribute) Z Zip (deepbiop.utils.CompressedType attribute) Zstd (deepbiop.utils.CompressedType attribute)