Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
W
_
_letlen (biseqt.sequence.Alphabet attribute)
_letters (biseqt.sequence.Alphabet attribute)
A
Aligner (class in biseqt.pw)
Alignment (class in biseqt.pw)
allowed_memory (biseqt.blot.WordBlotLocalRef attribute)
(biseqt.blot.WordBlotMultipleFast attribute)
(biseqt.blot.WordBlotOverlapRef attribute)
alphabet (biseqt.kmers.KmerDBWrapper attribute)
(biseqt.pw.Alignment attribute)
(biseqt.sequence.Sequence attribute)
(biseqt.stochastics.MutationProcess attribute)
Alphabet (class in biseqt.sequence)
as_kmer_seq() (biseqt.kmers.KmerCache method)
(in module biseqt.kmers)
B
B_GLOBAL (in module biseqt.pw)
B_LOCAL (in module biseqt.pw)
B_OVERLAP (in module biseqt.pw)
band_radii() (in module biseqt.blot)
band_radius() (biseqt.blot.WordBlot method)
(biseqt.blot.WordBlotMultiple method)
(in module biseqt.blot)
BANDED_MODE (in module biseqt.pw)
biseqt (module)
biseqt.blot (module)
biseqt.kmers (module)
biseqt.pw (module)
biseqt.seeds (module)
biseqt.sequence (module)
biseqt.stochastics (module)
biseqt.util (module)
C
cache (biseqt.kmers.KmerIndex attribute)
(biseqt.seeds.SeedIndex attribute)
(biseqt.seeds.SeedIndexMultiple attribute)
cached_seqs() (biseqt.kmers.KmerCache method)
calculate_score() (biseqt.pw.Aligner method)
(biseqt.pw.Alignment method)
call_svs() (in module experiments.blot_sv)
connection() (biseqt.kmers.KmerDBWrapper method)
content_id (biseqt.sequence.Sequence attribute)
contents (biseqt.sequence.Sequence attribute)
create_sql_index() (biseqt.kmers.KmerIndex method)
D
dptable_free (C function)
dptable_init (C function)
dptable_solve (C function)
dptable_traceback (C function)
drop_data() (biseqt.kmers.KmerIndex method)
E
END_ANCHORED (in module biseqt.pw)
END_ANCHORED_OVERLAP (in module biseqt.pw)
estimate_match_probability() (biseqt.blot.WordBlot method)
(biseqt.blot.WordBlotMultiple method)
exp_biological_multiple_sequences() (in module experiments.multiple_sequence)
exp_comp_aligned_genes() (in module experiments.blot_stats)
exp_count_seeds() (in module experiments.num_seeds)
exp_count_seeds_segment() (in module experiments.num_seeds)
exp_gap_probs() (in module experiments.band_radius)
exp_ig_genotyping() (in module experiments.blot_ig_genotyping)
exp_overlap_sequencing_reads() (in module experiments.blot_overlaps)
exp_overlap_simulations() (in module experiments.blot_overlaps)
exp_rearrangement() (in module experiments.blot_rearrangement)
exp_simulated_K_p() (in module experiments.blot_stats)
(in module experiments.multiple_sequence)
exp_structural_variants() (in module experiments.blot_sv)
exp_time_in_band() (in module experiments.band_radius)
exp_transposable_elements() (in module experiments.blot_te)
expected_overlap_len() (in module biseqt.blot)
experiments.band_radius (module)
experiments.blot_ig_genotyping (module)
experiments.blot_overlaps (module)
experiments.blot_rearrangement (module)
experiments.blot_stats (module)
experiments.blot_sv (module)
experiments.blot_te (module)
experiments.multiple_sequence (module)
experiments.num_seeds (module)
F
f (biseqt.util.ProgressIndicator attribute)
ffi (in module biseqt.pw)
find_all_neighbors() (biseqt.blot.WordBlot class method)
(biseqt.blot.WordBlotMultiple method)
find_peaks() (in module biseqt.blot)
finish() (biseqt.util.ProgressIndicator method)
G
g_max (biseqt.blot.WordBlot attribute)
(biseqt.blot.WordBlotMultiple attribute)
ge_prob (biseqt.stochastics.MutationProcess attribute)
GLOBAL (in module biseqt.pw)
go_prob (biseqt.stochastics.MutationProcess attribute)
H
H0_moments() (in module biseqt.blot)
H1_moments() (in module biseqt.blot)
highest_scoring_overlap_band() (biseqt.blot.WordBlotOverlap method)
(biseqt.blot.WordBlotOverlapRef method)
hits() (biseqt.kmers.KmerIndex method)
I
index_kmers() (biseqt.kmers.KmerIndex method)
init_script (biseqt.kmers.KmerDBWrapper attribute)
insert_dist (biseqt.stochastics.MutationProcess attribute)
K
kmer_as_int() (in module biseqt.kmers)
KmerCache (class in biseqt.kmers)
KmerDBWrapper (class in biseqt.kmers)
KmerIndex (class in biseqt.kmers)
kmers() (biseqt.kmers.KmerIndex method)
kmers_table (biseqt.kmers.KmerCache attribute)
(biseqt.kmers.KmerIndex attribute)
L
letter_to_idx() (biseqt.sequence.Alphabet method)
lib (in module biseqt.pw)
LOCAL (in module biseqt.pw)
log() (biseqt.kmers.KmerDBWrapper method)
(biseqt.util.Logger method)
log_odds_scores() (biseqt.stochastics.MutationProcess method)
log_table (biseqt.kmers.KmerIndex attribute)
Logger (class in biseqt.util)
M
mask (biseqt.kmers.KmerDBWrapper attribute)
mutant (biseqt.pw.Alignment attribute)
mutant_start (biseqt.pw.Alignment attribute)
mutate() (biseqt.stochastics.MutationProcess method)
MutationProcess (class in biseqt.stochastics)
N
name (biseqt.kmers.KmerDBWrapper attribute)
(biseqt.kmers.KmerIndex attribute)
noisy_read() (biseqt.stochastics.MutationProcess method)
num_total (biseqt.util.ProgressIndicator attribute)
O
origin (biseqt.pw.Alignment attribute)
origin_start (biseqt.pw.Alignment attribute)
OVERLAP (in module biseqt.pw)
P
parse() (biseqt.sequence.Alphabet method)
path (biseqt.kmers.KmerDBWrapper attribute)
percentage (biseqt.util.ProgressIndicator attribute)
progress() (biseqt.util.ProgressIndicator method)
ProgressIndicator (class in biseqt.util)
projected_len() (biseqt.pw.Alignment class method)
R
rand_read() (in module biseqt.stochastics)
rand_seq() (in module biseqt.stochastics)
render_term() (biseqt.pw.Alignment method)
reverse() (biseqt.sequence.Sequence method)
S
S (biseqt.seeds.SeedIndex attribute)
safe_malloc (C function)
score (biseqt.pw.Alignment attribute)
score_num_seeds() (biseqt.blot.WordBlot method)
(biseqt.blot.WordBlotMultiple method)
score_seeds() (biseqt.blot.WordBlot method)
(biseqt.blot.WordBlotMultiple method)
(biseqt.blot.WordBlotOverlap method)
score_seeds_() (biseqt.blot.WordBlotLocalRef method)
(biseqt.blot.WordBlotOverlapRef method)
seed_count() (biseqt.blot.WordBlotLocalRef method)
(biseqt.blot.WordBlotMultipleFast method)
(biseqt.blot.WordBlotOverlapRef method)
(biseqt.seeds.SeedIndex method)
(biseqt.seeds.SeedIndexMultiple method)
SeedIndex (class in biseqt.seeds)
SeedIndexMultiple (class in biseqt.seeds)
seeds() (biseqt.blot.WordBlotLocalRef method)
(biseqt.blot.WordBlotMultipleFast method)
(biseqt.blot.WordBlotOverlapRef method)
(biseqt.seeds.SeedIndex method)
(biseqt.seeds.SeedIndexMultiple method)
seeds_table (biseqt.seeds.SeedIndex attribute)
(biseqt.seeds.SeedIndexMultiple attribute)
segment_dims() (biseqt.blot.WordBlot method)
sensitivity (biseqt.blot.WordBlot attribute)
(biseqt.blot.WordBlotMultiple attribute)
seqs (biseqt.seeds.SeedIndexMultiple attribute)
Sequence (class in biseqt.sequence)
setup_ffi() (in module biseqt.pw)
similar_segments() (biseqt.blot.WordBlot method)
(biseqt.blot.WordBlotLocalRef method)
(biseqt.blot.WordBlotMultiple method)
solve() (biseqt.pw.Aligner method)
start() (biseqt.util.ProgressIndicator method)
START_ANCHORED (in module biseqt.pw)
START_ANCHORED_OVERLAP (in module biseqt.pw)
status() (biseqt.util.ProgressIndicator method)
STD_MODE (in module biseqt.pw)
subst_probs (biseqt.stochastics.MutationProcess attribute)
T
T (biseqt.seeds.SeedIndex attribute)
table_scores() (biseqt.pw.Aligner method)
to_diagonal_coordinates() (biseqt.seeds.SeedIndex class method)
(biseqt.seeds.SeedIndexMultiple class method)
to_ij_coordinates() (biseqt.seeds.SeedIndex class method)
(biseqt.seeds.SeedIndexMultiple class method)
to_ij_coordinates_seg() (biseqt.seeds.SeedIndex class method)
(biseqt.seeds.SeedIndexMultiple class method)
traceback() (biseqt.pw.Aligner method)
transcript (biseqt.pw.Alignment attribute)
transform() (biseqt.sequence.Alphabet method)
(biseqt.sequence.Sequence method)
truncate_to_match() (biseqt.pw.Alignment method)
W
wall_to_wall_distance() (biseqt.blot.WordBlotMultiple method)
(in module biseqt.blot)
WordBlot (class in biseqt.blot)
WordBlotLocalRef (class in biseqt.blot)
WordBlotMultiple (class in biseqt.blot)
WordBlotMultipleFast (class in biseqt.blot)
WordBlotOverlap (class in biseqt.blot)
WordBlotOverlapRef (class in biseqt.blot)
wordlen (biseqt.kmers.KmerDBWrapper attribute)
write() (biseqt.util.ProgressIndicator method)
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