Index A | B | C | D | E | F | G | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W A aa_coords_from_nt() (in module arda.refbuild.translate) allele (arda.refbuild.imgt.ImgtAllele attribute) Anchor (class in arda.cdr3fix) anchor_nt (arda.cdr3fix.Anchor attribute) anchors (arda.annotate.reference.Reference attribute) annotate_file() (in module arda.annotate.mapper) annotate_records() (in module arda.annotate.mapper) annotate_sequences() (in module arda.adapter) applied (arda.cdr3fix.Cdr3Error attribute) arda.adapter module arda.annotate.cigar module arda.annotate.contig module arda.annotate.dmap module arda.annotate.io module arda.annotate.mapper module arda.annotate.reference module arda.annotate.transfer module arda.cdr3fix module arda.dpost module arda.igblast module arda.mmseqs module arda.refbuild.build module arda.refbuild.combinations module arda.refbuild.imgt module arda.refbuild.translate module arda.rnaseq.assemble module arda.rnaseq.correct module arda.rnaseq.map module as_dict() (arda.rnaseq.assemble.AssembleReport method) (arda.rnaseq.correct.CorrectReport method) (arda.rnaseq.map.RnaseqReport method) assemble_contigs() (in module arda.rnaseq.assemble) AssembleReport (class in arda.rnaseq.assemble) B back_translate() (in module arda.refbuild.translate) build() (in module arda.refbuild.build) build_cigar() (in module arda.annotate.cigar) build_index() (in module arda.annotate.mapper) build_locus_scaffolds() (in module arda.refbuild.combinations) build_species() (in module arda.refbuild.build) by_gene (arda.dpost.DPosterior attribute) C c_call (arda.annotate.reference.RefEntry attribute) called (arda.annotate.dmap.DCall property) cdr3 (arda.cdr3fix.Cdr3Markup attribute) cdr3_repaired (arda.cdr3fix.Cdr3Markup attribute) Cdr3Error (class in arda.cdr3fix) Cdr3Markup (class in arda.cdr3fix) check_cigar() (in module arda.annotate.cigar) chunked() (in module arda.annotate.io) cigar_query_length() (in module arda.annotate.cigar) cigar_reference_length() (in module arda.annotate.cigar) clonotypes_in (arda.rnaseq.correct.CorrectReport attribute) clonotypes_out (arda.rnaseq.correct.CorrectReport attribute) collapsed (arda.rnaseq.correct.CorrectReport attribute) confident (arda.dpost.DPosterior property) constant_only_fragments (arda.rnaseq.map.RnaseqReport attribute) Contig (class in arda.annotate.contig) contigs (arda.rnaseq.assemble.AssembleReport attribute) contigs_complete (arda.rnaseq.assemble.AssembleReport attribute) convertalis() (in module arda.mmseqs) correct_airr() (in module arda.rnaseq.correct) CorrectReport (class in arda.rnaseq.correct) createdb() (in module arda.mmseqs) D d2_call (arda.annotate.dmap.DCall attribute) d2_sequence_end (arda.annotate.dmap.DCall attribute) d2_sequence_start (arda.annotate.dmap.DCall attribute) d2_support (arda.annotate.dmap.DCall attribute) d_call (arda.annotate.dmap.DCall attribute) (arda.dpost.DPosterior attribute) d_germlines (arda.annotate.reference.Reference attribute) d_sequence_end (arda.annotate.dmap.DCall attribute) d_sequence_start (arda.annotate.dmap.DCall attribute) d_start (arda.dpost.DPosterior attribute) d_start_ci90 (arda.dpost.DPosterior attribute) d_support (arda.annotate.dmap.DCall attribute) DCall (class in arda.annotate.dmap) detect_coding_frame() (in module arda.refbuild.translate) detect_format() (in module arda.annotate.io) dist (arda.cdr3fix.Cdr3Error attribute) download_reference() (in module arda.refbuild.imgt) DPosterior (class in arda.dpost) E easy_search() (in module arda.mmseqs) edit_imgt_file() (in module arda.igblast) ends (arda.annotate.reference.RefEntry attribute) entries (arda.annotate.reference.Reference attribute) entropy (arda.dpost.DPosterior attribute) errors (arda.cdr3fix.Cdr3Markup attribute) explain() (arda.cdr3fix.Cdr3Markup method) extra (arda.annotate.dmap.DCall attribute) F fix_needed (arda.cdr3fix.Cdr3Markup property) format_report() (in module arda.cdr3fix) frm (arda.cdr3fix.Cdr3Error attribute) functionality (arda.cdr3fix.Anchor attribute) (arda.refbuild.imgt.ImgtAllele attribute) G gene_fasta_path() (in module arda.refbuild.imgt) germline_nt (arda.cdr3fix.Anchor attribute) get() (arda.annotate.reference.Reference method) good (arda.cdr3fix.Cdr3Markup property) I IgBlastError igblastn_airr() (in module arda.igblast) igdata_env() (in module arda.igblast) ImgtAllele (class in arda.refbuild.imgt) input (arda.rnaseq.map.RnaseqReport attribute) is_dd (arda.annotate.dmap.DCall property) is_functional (arda.refbuild.imgt.ImgtAllele property) is_jc (arda.annotate.reference.RefEntry property) isotype_from_mate (arda.rnaseq.map.RnaseqReport attribute) J j_call (arda.annotate.reference.RefEntry attribute) (arda.cdr3fix.Cdr3Markup attribute) j_calls (arda.refbuild.combinations.Scaffold attribute) j_canonical (arda.cdr3fix.Cdr3Markup property) j_fix (arda.cdr3fix.Cdr3Markup attribute) j_sequence_start (arda.annotate.dmap.DCall attribute) (arda.annotate.reference.RefEntry attribute) j_start (arda.cdr3fix.Cdr3Markup attribute) K kind (arda.cdr3fix.Cdr3Error attribute) L length (arda.cdr3fix.Cdr3Error attribute) load_anchors() (in module arda.cdr3fix) load_d_prior() (in module arda.dpost) load_j_fr4_offsets() (in module arda.refbuild.combinations) load_j_frames() (in module arda.refbuild.combinations) load_reference() (in module arda.annotate.reference) load_v_fwr3_stops() (in module arda.refbuild.combinations) locus (arda.annotate.dmap.DCall attribute) (arda.annotate.reference.RefEntry attribute) (arda.cdr3fix.Anchor attribute) (arda.cdr3fix.Cdr3Markup attribute) (arda.dpost.DPosterior attribute) (arda.refbuild.combinations.Scaffold attribute) M makeblastdb() (in module arda.igblast) map_d_junction() (in module arda.annotate.dmap) map_rnaseq() (in module arda.rnaseq.map) mapped_fraction (arda.rnaseq.map.RnaseqReport property) mapped_reads (arda.rnaseq.map.RnaseqReport attribute) markup_batch() (in module arda.cdr3fix) markup_cdr3() (in module arda.cdr3fix) markup_records() (in module arda.cdr3fix) merge_contig() (in module arda.annotate.contig) merge_contigs() (in module arda.annotate.contig) merge_pair() (in module arda.rnaseq.map) min_score (arda.rnaseq.map.RnaseqReport attribute) mmseqs_binary() (in module arda.mmseqs) MMseqsError module arda.adapter arda.annotate.cigar arda.annotate.contig arda.annotate.dmap arda.annotate.io arda.annotate.mapper arda.annotate.reference arda.annotate.transfer arda.cdr3fix arda.dpost arda.igblast arda.mmseqs arda.refbuild.build arda.refbuild.combinations arda.refbuild.imgt arda.refbuild.translate arda.rnaseq.assemble arda.rnaseq.correct arda.rnaseq.map N n_middle_nt (arda.dpost.DPosterior attribute) n_pad (arda.refbuild.combinations.Scaffold attribute) np1 (arda.annotate.dmap.DCall attribute) np2 (arda.annotate.dmap.DCall attribute) np3 (arda.annotate.dmap.DCall attribute) O offset (arda.annotate.contig.ReadPlacement attribute) open_text() (in module arda.annotate.io) organism (arda.annotate.reference.Reference attribute) (arda.rnaseq.map.RnaseqReport attribute) P parse_cigar() (in module arda.annotate.cigar) parse_functionality() (in module arda.refbuild.imgt) partial_nt (arda.cdr3fix.Anchor attribute) peak_rss_mb (arda.rnaseq.map.RnaseqReport attribute) per_locus (arda.rnaseq.map.RnaseqReport attribute) pos (arda.cdr3fix.Cdr3Error attribute) posterior (arda.dpost.DPosterior attribute) posterior_d() (in module arda.dpost) Q qaln (arda.annotate.contig.ReadPlacement attribute) qstart (arda.annotate.contig.ReadPlacement attribute) R read_fasta() (in module arda.refbuild.imgt) read_pairs() (in module arda.rnaseq.map) read_sequences() (in module arda.annotate.io) ReadPlacement (class in arda.annotate.contig) reads (arda.annotate.contig.Contig attribute) (arda.rnaseq.correct.CorrectReport attribute) reads_in (arda.rnaseq.assemble.AssembleReport attribute) reads_incomplete (arda.rnaseq.correct.CorrectReport attribute) reads_per_second (arda.rnaseq.map.RnaseqReport attribute) reads_rescued (arda.rnaseq.assemble.AssembleReport attribute) reads_with_junction (arda.rnaseq.correct.CorrectReport attribute) reannotate_contigs() (in module arda.annotate.contig) RefEntry (class in arda.annotate.reference) Reference (class in arda.annotate.reference) reverse_complement() (in module arda.refbuild.translate) RnaseqReport (class in arda.rnaseq.map) run() (in module arda.mmseqs) S Scaffold (class in arda.refbuild.combinations) scaffold_id (arda.refbuild.combinations.Scaffold attribute) search() (in module arda.mmseqs) seeds (arda.rnaseq.assemble.AssembleReport attribute) segment (arda.cdr3fix.Anchor attribute) segment_cigars() (in module arda.annotate.cigar) seqtype (arda.annotate.reference.Reference attribute) sequence (arda.annotate.contig.Contig attribute) (arda.refbuild.combinations.Scaffold attribute) (arda.refbuild.imgt.ImgtAllele attribute) sequence_id (arda.annotate.contig.Contig attribute) (arda.cdr3fix.Cdr3Markup attribute) side (arda.cdr3fix.Cdr3Error attribute) source (arda.cdr3fix.Anchor attribute) species (arda.cdr3fix.Cdr3Markup attribute) starts (arda.annotate.reference.RefEntry attribute) status (arda.cdr3fix.Anchor attribute) support_aa (arda.dpost.DPosterior attribute) T taln (arda.annotate.contig.ReadPlacement attribute) target (arda.annotate.contig.Contig attribute) target_fasta (arda.annotate.reference.Reference attribute) templated_aa (arda.cdr3fix.Anchor attribute) threads (arda.rnaseq.map.RnaseqReport attribute) to (arda.cdr3fix.Cdr3Error attribute) to_cdr3fix() (arda.cdr3fix.Cdr3Markup method) to_frame() (in module arda.cdr3fix) tool() (in module arda.igblast) top_hit() (in module arda.mmseqs) total_reads (arda.rnaseq.map.RnaseqReport attribute) transfer_hit() (in module arda.annotate.transfer) translate() (in module arda.refbuild.translate) tstart (arda.annotate.contig.ReadPlacement attribute) U ungap_gene() (in module arda.refbuild.imgt) V v_call (arda.annotate.reference.RefEntry attribute) (arda.cdr3fix.Cdr3Markup attribute) v_calls (arda.refbuild.combinations.Scaffold attribute) v_canonical (arda.cdr3fix.Cdr3Markup property) v_end (arda.cdr3fix.Cdr3Markup attribute) v_fix (arda.cdr3fix.Cdr3Markup attribute) v_sequence_end (arda.annotate.dmap.DCall attribute) (arda.annotate.reference.RefEntry attribute) version() (in module arda.mmseqs) version_key() (in module arda.mmseqs) vj_end (arda.annotate.reference.RefEntry attribute) W wall_seconds (arda.rnaseq.map.RnaseqReport attribute) write_fasta() (in module arda.annotate.io)