Index

A | B | C | D | E | F | G | H | I | L | M | N | O | P | Q | R | S | T | U | V | W | X

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 method)
first_last1() (Interval 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 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)