Index
A
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C
|
D
|
G
|
H
|
I
|
L
|
M
|
N
|
P
|
Q
|
R
|
S
|
T
|
V
|
W
A
adapter_b (spats_shape_seq.run.Run attribute)
adapter_t (spats_shape_seq.run.Run attribute)
addTagPlugin() (spats_shape_seq.reads.ReadsAnalyzer method)
addTagTarget() (spats_shape_seq.reads.ReadsAnalyzer method)
addTarget() (spats_shape_seq.spats.Spats method)
addTargets() (spats_shape_seq.spats.Spats method)
algorithm (spats_shape_seq.run.Run attribute)
allow_indeterminate (spats_shape_seq.run.Run attribute)
allow_multiple_rt_starts (spats_shape_seq.run.Run attribute)
allow_negative_values (spats_shape_seq.run.Run attribute)
allowed_adapter_errors (spats_shape_seq.run.Run attribute)
allowed_dumbbell_errors (spats_shape_seq.run.Run attribute)
allowed_target_errors (spats_shape_seq.run.Run attribute)
apply_config_restrictions() (spats_shape_seq.run.Run method)
C
collapse_left_prefixes (spats_shape_seq.run.Run attribute)
collapse_only_prefixes (spats_shape_seq.run.Run attribute)
compare_results() (spats_shape_seq.spats.Spats method)
compute_profiles() (spats_shape_seq.spats.Spats method)
compute_z_reactivity (spats_shape_seq.run.Run attribute)
config_dict() (spats_shape_seq.run.Run method)
config_string() (spats_shape_seq.run.Run method)
cotrans (spats_shape_seq.run.Run attribute)
cotrans_linker (spats_shape_seq.run.Run attribute)
cotrans_minimum_length (spats_shape_seq.run.Run attribute)
count_edge_mutations (spats_shape_seq.run.Run attribute)
count_left_prefixes (spats_shape_seq.run.Run attribute)
count_mutations (spats_shape_seq.run.Run attribute)
count_only_full_reads (spats_shape_seq.run.Run attribute)
counters (spats_shape_seq.spats.Spats attribute)
D
debug (spats_shape_seq.run.Run attribute)
dumbbell (spats_shape_seq.run.Run attribute)
G
generate_channel_reads (spats_shape_seq.run.Run attribute)
generate_sam (spats_shape_seq.run.Run attribute)
H
handle_indels (spats_shape_seq.run.Run attribute)
I
ignore_stops_with_mismatched_overlap (spats_shape_seq.run.Run attribute)
indel_gap_extend_cost (spats_shape_seq.run.Run attribute)
indel_gap_open_cost (spats_shape_seq.run.Run attribute)
indel_match_value (spats_shape_seq.run.Run attribute)
indel_mismatch_cost (spats_shape_seq.run.Run attribute)
L
load() (spats_shape_seq.spats.Spats method)
load_from_config() (spats_shape_seq.run.Run method)
loadTargets() (spats_shape_seq.spats.Spats method)
log (spats_shape_seq.run.Run attribute)
M
masks (spats_shape_seq.run.Run attribute)
merge() (spats_shape_seq.spats.Spats method)
merge_targets() (spats_shape_seq.spats.Spats method)
minimum_adapter_len (spats_shape_seq.run.Run attribute)
minimum_tag_match_length (spats_shape_seq.run.Run attribute)
minimum_target_match_length (spats_shape_seq.run.Run attribute)
mutations_require_quality_score (spats_shape_seq.run.Run attribute)
N
num_workers (spats_shape_seq.run.Run attribute)
P
pair_db (spats_shape_seq.reads.ReadsData attribute)
pair_length (spats_shape_seq.run.Run attribute)
parse() (spats_shape_seq.reads.ReadsData method)
process_pair() (spats_shape_seq.spats.Spats method)
process_pair_data() (spats_shape_seq.spats.Spats method)
process_pair_db() (spats_shape_seq.spats.Spats method)
process_tags() (spats_shape_seq.reads.ReadsAnalyzer method)
Q
quiet (spats_shape_seq.run.Run attribute)
R
ReadsAnalyzer (class in spats_shape_seq.reads)
ReadsData (class in spats_shape_seq.reads)
regions_of_interest (spats_shape_seq.run.Run attribute)
reset_processor() (spats_shape_seq.spats.Spats method)
result_set_name (spats_shape_seq.run.Run attribute)
resume_processing (spats_shape_seq.run.Run attribute)
rt_primers (spats_shape_seq.run.Run attribute)
Run (class in spats_shape_seq.run)
run (spats_shape_seq.reads.ReadsAnalyzer attribute)
run_spats() (in module spats_shape_seq)
S
single_target_linker (spats_shape_seq.run.Run attribute)
skip_database (spats_shape_seq.run.Run attribute)
Spats (class in spats_shape_seq.spats)
spats_shape_seq (module)
,
[1]
spats_shape_seq.reads (module)
store() (spats_shape_seq.spats.Spats method)
T
tag_counts() (spats_shape_seq.reads.ReadsAnalyzer method)
targets (spats_shape_seq.spats.Spats attribute)
V
validate_config() (spats_shape_seq.run.Run method)
validate_results() (spats_shape_seq.spats.Spats method)
W
write_reactivities() (spats_shape_seq.spats.Spats method)
writeback_results (spats_shape_seq.run.Run attribute)
Spats
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See also:
Installation
Quickstart Guide
spats_tool
Advanced Usage
Spats
Reads Analyzer
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