Index

A

Aa_substitution (class in vdjml._vdjml_py) aa_substitutions() (Segment_match method) Aa_substitutions_set (class in vdjml._vdjml_py) aligner() (Gene_region method) (Gl_segment_match method)

Aligner_id (class in vdjml._vdjml_py) Aligner_info (class in vdjml._vdjml_py) Aligner_map (class in vdjml._vdjml_py) aligner_map() (Results_meta method)

B

Btop (class in vdjml._vdjml_py) btop() (Segment_match method)

Btop_stats (class in vdjml._vdjml_py) buff_size (Xml_writer_options attribute)

C

Codon_match (class in vdjml._vdjml_py) codons() (in module vdjml._vdjml_py)

comp_dna() (in module vdjml.igblast_parse) compareIGBlastJuncDataWithQueryJuncData() (in module vdjml.igblast_parse)

D

datetime() (Vdjml_generator_info method) datetime_str() (Vdjml_generator_info method)

deletions() (Match_metrics method) deletions_ (Btop_stats attribute)

E

empty() (Aa_substitutions_set method) (Aligner_map method) (Btop method) (Gene_region_map method) (Gene_region_set method) (Germline_db_map method) (Gl_segment_map method) (Num_system_map method) (Result_store method) (Segment_match_id_set method) (Segment_match_map method) end_ (Sequence_match attribute) extractAsItemOrFirstFromList() (in module vdjml.igblast_parse)

extractJunctionRegionSeq() (in module vdjml.igblast_parse) extractSubSeq() (in module vdjml.igblast_parse)

F

first_last0() (Interval static method) first_last1() (Interval static method)

frame_shift() (Match_metrics method)

G

Gene_region (class in vdjml._vdjml_py) Gene_region_map (class in vdjml._vdjml_py) gene_region_map() (Results_meta method) Gene_region_set (class in vdjml._vdjml_py) generator_info() (Vdjml_reader method) Germline_db_map (class in vdjml._vdjml_py) get() (Result_builder method) (Segment_match_builder method) getRevCompInterval() (in module vdjml.igblast_parse) getSubstitutionsInsertionsDeletionsFromBTOP() (in module vdjml.igblast_parse) gl_aa() (Aa_substitution method) gl_char() (Codon_match method) gl_database() (Gl_segment_info method) Gl_db_id (class in vdjml._vdjml_py) Gl_db_info (class in vdjml._vdjml_py) gl_db_map() (Results_meta method)

gl_len_ (Btop_stats attribute) gl_length() (Segment_match method) gl_nuc() (Codon_match method) (Nucleotide_match method) gl_pos() (Codon_match method) (Nucleotide_match method) gl_position() (Gl_segment_match method) gl_range() (Segment_match method) Gl_seg_id (class in vdjml._vdjml_py) Gl_seg_match_id (class in vdjml._vdjml_py) gl_segment() (Gl_segment_match method) Gl_segment_info (class in vdjml._vdjml_py) Gl_segment_map (class in vdjml._vdjml_py) gl_segment_map() (Results_meta method) Gl_segment_match (class in vdjml._vdjml_py) gl_segments() (Segment_match method)

H

has_result() (Vdjml_reader method)

I

id() (Aligner_info method) (Gl_db_info method) (Gl_segment_info method) (Gl_segment_match method) (Read_result method) (Segment_match method) identity() (Match_metrics method) indent (Xml_writer_options attribute) insert() (Read_result method) (Result_store method) (Results_meta method) (Segment_combination method) (Segment_match method) insert_aa_substitution() (Segment_match_builder method) insert_gl_segment_match() (Segment_match_builder method) insert_region() (Segment_combination_builder method) insert_segment_combination() (Result_builder method) insert_segment_match() (Result_builder method) insertions() (Match_metrics method) insertions_ (Btop_stats attribute)

Interval (class in vdjml._vdjml_py) inverted() (Match_metrics method) is_deletion() (Nucleotide_match method) is_gl_contiguous() (Codon_match method) is_gl_translatable() (Codon_match method) is_insertion() (Nucleotide_match method) is_match() (Codon_match method) (Nucleotide_match method) is_read_contiguous() (Codon_match method) is_read_translatable() (Codon_match method) is_silent() (Codon_match method) is_translatable() (Codon_match method)

L

last0() (Interval method) last1() (Interval method)

length() (Interval method)

M

makeMap() (in module vdjml.igblast_parse) makeMetricFromCharMap() (in module vdjml.igblast_parse) Match_metrics (class in vdjml._vdjml_py) match_metrics() (Gene_region method) (Segment_match method)

matches() (Btop_stats method) meta() (Result_store method) (Vdjml_reader method) mismatches() (in module vdjml._vdjml_py) mutated_invariant() (Match_metrics method)

N

name() (Aligner_info method) (Gl_db_info method) (Gl_segment_info method) (Vdjml_generator_info method) new_result() (Result_factory method) next() (Vdjml_reader method) Nucleotide_match (class in vdjml._vdjml_py) nucleotide_match() (in module vdjml._vdjml_py) nucleotides() (in module vdjml._vdjml_py)

num_system() (Gl_segment_match method) Num_system_map (class in vdjml._vdjml_py) num_system_map() (Results_meta method) numbering_system() (Gene_region method) (in module vdjml._vdjml_py) Numsys_id (class in vdjml._vdjml_py)

O

obtainJuncIntervalAndSeq() (in module vdjml.igblast_parse) out_frame_indel() (Match_metrics method)

out_frame_vdj() (Match_metrics method)

P

parameters() (Aligner_info method) pos0() (Interval method) pos0_len() (Interval static method)

pos1() (Interval method) printMap() (in module vdjml.igblast_parse) productive() (Match_metrics method)

Q

quote (Xml_writer_options attribute)

R

read_aa() (Aa_substitution method) read_char() (Codon_match method) read_len_ (Btop_stats attribute) read_nuc() (Codon_match method) (Nucleotide_match method) read_pos() (Codon_match method) (Nucleotide_match method) read_position() (Aa_substitution method) read_range() (Gene_region method) (Segment_match method) Read_result (class in vdjml._vdjml_py) Region_id (class in vdjml._vdjml_py)

region_type() (Gene_region method) regions() (Segment_combination method) release() (Result_builder method) result() (Vdjml_reader method) Result_builder (class in vdjml._vdjml_py) Result_factory (class in vdjml._vdjml_py) Result_store (class in vdjml._vdjml_py) Results_meta (class in vdjml._vdjml_py) run_id() (Aligner_info method)

S

scanOutputToVDJML() (in module vdjml.igblast_parse) score() (Match_metrics method) Seg_match_id (class in vdjml._vdjml_py) Segment_combination (class in vdjml._vdjml_py) Segment_combination_builder (class in vdjml._vdjml_py) segment_combinations() (Read_result method) Segment_match (class in vdjml._vdjml_py) Segment_match_builder (class in vdjml._vdjml_py) Segment_match_id_set (class in vdjml._vdjml_py) Segment_match_map (class in vdjml._vdjml_py) segment_matches() (Read_result method) segment_name() (in module vdjml._vdjml_py) segment_type() (Gl_segment_info method) (in module vdjml._vdjml_py)

segments() (Segment_combination method) seq_ (Sequence_match attribute) Sequence_match (class in vdjml._vdjml_py) sequence_match() (in module vdjml._vdjml_py) set_default_aligner() (Result_factory method) set_default_gl_database() (Result_factory method) set_default_num_system() (Result_factory method) species() (Gl_db_info method) start_ (Sequence_match attribute) stop_codon() (Match_metrics method) substitutions() (Match_metrics method) substitutions_ (Btop_stats attribute)

T

translate_gl() (Codon_match method) translate_read() (Codon_match method)

trim_complement() (in module vdjml._vdjml_py)

U

uri() (Aligner_info method) (Gl_db_info method)

V

vdjml (module) vdjml._vdjml_py (module) vdjml.igblast_parse (module) Vdjml_generator_info (class in vdjml._vdjml_py)

Vdjml_reader (class in vdjml._vdjml_py) Vdjml_writer (class in vdjml._vdjml_py) version() (Aligner_info method) (Gl_db_info method) (Vdjml_generator_info method) (Vdjml_reader method) version_str() (Vdjml_reader method)

W

write_to_file() (in module vdjml._vdjml_py)

X

Xml_writer_options (class in vdjml._vdjml_py)