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Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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Z
A
about() (snipgenie.gui.App method)
accept() (snipgenie.widgets.MultipleInputDialog method)
add_dock() (snipgenie.gui.App method)
add_file() (snipgenie.gui.App method)
add_gc_mean() (snipgenie.gui.App method)
add_mapping_stats() (snipgenie.gui.App method)
add_mask() (snipgenie.gui.App method)
add_mean_depth() (snipgenie.gui.App method)
add_plugin_dock() (snipgenie.gui.App method)
add_read_lengths() (snipgenie.gui.App method)
add_recent_file() (snipgenie.gui.App method)
add_widgets() (snipgenie.widgets.BrowserViewer method)
(snipgenie.widgets.GraphicalBamViewer method)
(snipgenie.widgets.SimpleBamViewer method)
(snipgenie.widgets.TextViewer method)
addButton() (snipgenie.widgets.ToolBar method)
addToolBarItems() (in module snipgenie.widgets)
align_files() (snipgenie.gui.App method)
align_reads() (in module snipgenie.app)
alignment_completed() (snipgenie.gui.App method)
App (class in snipgenie.gui)
apply() (snipgenie.widgets.BaseOptions method)
(snipgenie.widgets.BasicDialog method)
(snipgenie.widgets.MergeDialog method)
(snipgenie.widgets.PreferencesDialog method)
applyOptions() (snipgenie.widgets.BaseOptions method)
AppOptions (class in snipgenie.gui)
artificial_fastq_generator() (in module snipgenie.simulate)
B
bam_to_fastq() (in module snipgenie.tools)
BaseOptions (class in snipgenie.widgets)
BasicDialog (class in snipgenie.widgets)
batch_iterator() (in module snipgenie.tools)
biopython_draw_tree() (in module snipgenie.trees)
blast_contaminants() (in module snipgenie.app)
blast_fasta() (in module snipgenie.tools)
blast_sequences() (in module snipgenie.tools)
bowtie_align() (in module snipgenie.aligners)
BrowserViewer (class in snipgenie.widgets)
build_bowtie_index() (in module snipgenie.aligners)
build_bwa_index() (in module snipgenie.aligners)
build_subread_index() (in module snipgenie.aligners)
bwa_align() (in module snipgenie.aligners)
C
calling_completed() (snipgenie.gui.App method)
check_contamination() (snipgenie.gui.App method)
check_fastq_table() (snipgenie.gui.App method)
check_files() (snipgenie.gui.App method)
check_heterozygosity() (snipgenie.gui.App method)
check_missing_files() (snipgenie.gui.App method)
check_output_folder() (snipgenie.gui.App method)
check_platform() (in module snipgenie.app)
check_samples_aligned() (in module snipgenie.app)
check_samples_unique() (in module snipgenie.app)
checkDict() (in module snipgenie.tools)
clean_bam_files() (in module snipgenie.app)
clean_up() (snipgenie.gui.App method)
clear() (snipgenie.widgets.PlotViewer method)
clear_plugins() (snipgenie.gui.App method)
clear_tabs() (snipgenie.gui.App method)
close() (snipgenie.widgets.BasicDialog method)
close_right_tab() (snipgenie.gui.App method)
close_tab() (snipgenie.gui.App method)
closeEvent() (snipgenie.gui.App method)
clustal_alignment() (in module snipgenie.tools)
color() (snipgenie.widgets.ColorButton method)
color_leaves() (in module snipgenie.trees)
ColorButton (class in snipgenie.widgets)
colorChanged (snipgenie.widgets.ColorButton attribute)
colors_from_labels() (in module snipgenie.trees)
Communicate (class in snipgenie.gui)
concat_seqrecords() (in module snipgenie.tools)
contextMenuEvent() (snipgenie.widgets.Editor method)
(snipgenie.widgets.PlainTextEditor method)
convert_branch_lengths() (in module snipgenie.trees)
copy_ref_genomes() (in module snipgenie.app)
copy_to_clipboard() (snipgenie.widgets.BasicDialog method)
core_alignment_from_vcf() (in module snipgenie.tools)
create_figure() (snipgenie.widgets.PlotViewer method)
create_grid() (in module snipgenie.plotting)
create_hex_grid() (in module snipgenie.plotting)
create_menu() (snipgenie.gui.App method)
create_tool_bar() (snipgenie.gui.App method)
create_tree() (in module snipgenie.trees)
createButtons() (snipgenie.widgets.BasicDialog method)
(snipgenie.widgets.PreferencesDialog method)
(snipgenie.widgets.ToolBar method)
createWidgets() (snipgenie.widgets.BasicDialog method)
(snipgenie.widgets.MergeDialog method)
(snipgenie.widgets.PreferencesDialog method)
csq_call() (in module snipgenie.app)
csq_viewer() (snipgenie.gui.App method)
D
dataframe_to_fasta() (in module snipgenie.tools)
delete_nodes() (in module snipgenie.trees)
dialogFromOptions() (in module snipgenie.widgets)
diffseqs() (in module snipgenie.tools)
discover_plugins() (snipgenie.gui.App method)
display_igv() (in module snipgenie.plotting)
draw_pie() (in module snipgenie.plotting)
DynamicDialog (class in snipgenie.widgets)
E
Editor (class in snipgenie.widgets)
error (snipgenie.gui.WorkerSignals attribute)
F
fasta_to_dataframe() (in module snipgenie.tools)
fastq_quality_report() (in module snipgenie.tools)
(snipgenie.gui.App method)
fastq_random_seqs() (in module snipgenie.tools)
fastq_to_dataframe() (in module snipgenie.tools)
fastq_to_fasta() (in module snipgenie.tools)
fastq_to_rec() (in module snipgenie.tools)
features_summary() (in module snipgenie.tools)
fetch_binaries() (in module snipgenie.app)
fetch_contam_file() (in module snipgenie.app)
fetch_sra_reads() (in module snipgenie.tools)
FileViewer (class in snipgenie.widgets)
find_gene() (snipgenie.widgets.SimpleBamViewer method)
finished (snipgenie.gui.WorkerSignals attribute)
flush() (snipgenie.app.Logger method)
format_nodes() (in module snipgenie.trees)
G
gen_colors() (in module snipgenie.plotting)
genbank_to_dataframe() (in module snipgenie.tools)
generate_fastqs() (in module snipgenie.simulate)
get_aa_snp_matrix() (in module snipgenie.app)
get_attributes() (in module snipgenie.tools)
get_bam_aln() (in module snipgenie.plotting)
get_blast_results() (in module snipgenie.tools)
get_chrom() (in module snipgenie.tools)
get_chrom_from_bam() (in module snipgenie.plotting)
get_clusters() (in module snipgenie.trees)
get_cmd() (in module snipgenie.tools)
get_color_mapping() (in module snipgenie.plotting)
get_colormap() (in module snipgenie.trees)
get_coverage() (in module snipgenie.plotting)
get_fasta_length() (in module snipgenie.plotting)
(in module snipgenie.tools)
get_fasta_names() (in module snipgenie.plotting)
get_fasta_reads() (snipgenie.gui.App method)
get_fasta_sequence() (in module snipgenie.plotting)
get_fastq_info() (in module snipgenie.tools)
get_fastq_read_lengths() (in module snipgenie.tools)
get_fastq_size() (in module snipgenie.tools)
get_files_from_paths() (in module snipgenie.app)
get_gc() (in module snipgenie.tools)
get_mean_depth() (in module snipgenie.tools)
get_pivoted_samples() (in module snipgenie.app)
get_right_tabs() (snipgenie.gui.App method)
get_samples() (in module snipgenie.app)
get_samples_from_bam() (in module snipgenie.app)
get_sb_number() (in module snipgenie.tools)
get_selected() (snipgenie.gui.App method)
get_snp_matrix() (in module snipgenie.tools)
get_spoligotype() (in module snipgenie.tools)
get_spoligotypes() (in module snipgenie.tools)
get_subsample_reads() (in module snipgenie.tools)
get_tab_indices() (snipgenie.gui.App method)
get_tab_names() (snipgenie.gui.App method)
get_tabs() (snipgenie.gui.App method)
get_unique_snps() (in module snipgenie.tools)
get_values() (snipgenie.widgets.DynamicDialog method)
get_vcf_samples() (in module snipgenie.tools)
getWidgetValues() (in module snipgenie.widgets)
gff_bcftools_format() (in module snipgenie.tools)
gff_to_records() (in module snipgenie.tools)
goto() (snipgenie.widgets.SimpleBamViewer method)
GraphicalBamViewer (class in snipgenie.widgets)
gunzip() (in module snipgenie.tools)
H
heatmap() (in module snipgenie.plotting)
I
import_results_folder() (snipgenie.gui.App method)
increment() (snipgenie.widgets.BaseOptions method)
insert() (snipgenie.widgets.Editor method)
K
kraken() (in module snipgenie.tools)
L
load_data() (snipgenie.widgets.GraphicalBamViewer method)
(snipgenie.widgets.SimpleBamViewer method)
load_fastq_files_dialog() (snipgenie.gui.App method)
load_fastq_folder_dialog() (snipgenie.gui.App method)
load_fastq_table() (snipgenie.gui.App method)
load_page() (snipgenie.widgets.BrowserViewer method)
load_plugin() (snipgenie.gui.App method)
load_preset_genome() (snipgenie.gui.App method)
load_presets_menu() (snipgenie.gui.App method)
load_project() (snipgenie.gui.App method)
load_project_dialog() (snipgenie.gui.App method)
load_settings() (snipgenie.gui.App method)
load_test() (snipgenie.gui.App method)
local_blast() (in module snipgenie.tools)
Logger (class in snipgenie.app)
M
main() (in module snipgenie.app)
(in module snipgenie.gui)
make_blast_database() (in module snipgenie.tools)
make_legend() (in module snipgenie.plotting)
make_phylo_tree() (snipgenie.gui.App method)
mapping_stats() (in module snipgenie.app)
(snipgenie.gui.App method)
mask_filter() (in module snipgenie.app)
merge_meta_data() (snipgenie.gui.App method)
MergeDialog (class in snipgenie.widgets)
minimap2_align() (in module snipgenie.aligners)
missing_sites() (snipgenie.gui.App method)
module
snipgenie
snipgenie.aligners
snipgenie.app
snipgenie.gui
snipgenie.plotting
snipgenie.simulate
snipgenie.tools
snipgenie.trees
snipgenie.widgets
mousePressEvent() (snipgenie.widgets.ColorButton method)
move_files() (in module snipgenie.tools)
mpileup() (in module snipgenie.app)
mpileup_multiprocess() (in module snipgenie.app)
mpileup_parallel() (in module snipgenie.app)
mpileup_region() (in module snipgenie.app)
MultipleInputDialog (class in snipgenie.widgets)
N
navigate_to_url() (snipgenie.widgets.BrowserViewer method)
new_project() (snipgenie.gui.App method)
newproj (snipgenie.gui.Communicate attribute)
next_page() (snipgenie.widgets.SimpleBamViewer method)
normpdf() (in module snipgenie.tools)
O
onColorPicker() (snipgenie.widgets.ColorButton method)
online_documentation() (snipgenie.gui.App method)
overwrite_vcf() (in module snipgenie.app)
P
pdf_qc_reports() (in module snipgenie.tools)
phylogeny_completed() (snipgenie.gui.App method)
PlainTextEditor (class in snipgenie.widgets)
plot_bam_alignment() (in module snipgenie.plotting)
plot_coverage() (in module snipgenie.plotting)
plot_dist_matrix() (snipgenie.gui.App method)
plot_fastq_gc_content() (in module snipgenie.tools)
plot_fastq_qualities() (in module snipgenie.tools)
plot_features() (in module snipgenie.plotting)
PlotViewer (class in snipgenie.widgets)
preferences() (snipgenie.gui.App method)
PreferencesDialog (class in snipgenie.widgets)
prev_page() (snipgenie.widgets.SimpleBamViewer method)
printOccur (snipgenie.gui.StdoutRedirect attribute)
processing_completed() (snipgenie.gui.App method)
progress (snipgenie.gui.WorkerSignals attribute)
progress_fn() (snipgenie.gui.App method)
Q
quality_summary() (snipgenie.gui.App method)
quit() (snipgenie.gui.App method)
R
random_colors() (in module snipgenie.plotting)
rd_analysis() (snipgenie.gui.App method)
rd_analysis_completed() (snipgenie.gui.App method)
read_csq_file() (in module snipgenie.app)
read_distributon() (snipgenie.gui.App method)
records_to_dataframe() (in module snipgenie.tools)
redirect_stdout() (snipgenie.gui.App method)
redraw() (snipgenie.widgets.GraphicalBamViewer method)
(snipgenie.widgets.PlotViewer method)
(snipgenie.widgets.SimpleBamViewer method)
relabel_vcfheader() (in module snipgenie.app)
remote_blast() (in module snipgenie.tools)
remove_nodes() (in module snipgenie.trees)
remove_tiplabels() (in module snipgenie.trees)
reset() (snipgenie.widgets.PreferencesDialog method)
resource_path() (in module snipgenie.tools)
result (snipgenie.gui.WorkerSignals attribute)
run() (snipgenie.app.WorkFlow method)
(snipgenie.gui.App method)
(snipgenie.gui.Worker method)
run_bamfiles() (in module snipgenie.app)
run_fasttree() (in module snipgenie.trees)
run_phastsim() (in module snipgenie.simulate)
run_RAXML() (in module snipgenie.trees)
run_threaded_process() (snipgenie.gui.App method)
run_treecluster() (in module snipgenie.trees)
run_trimming() (snipgenie.gui.App method)
S
sample_details() (snipgenie.gui.App method)
samtools_coverage() (in module snipgenie.tools)
samtools_depth() (in module snipgenie.tools)
samtools_flagstat() (in module snipgenie.tools)
samtools_tview() (in module snipgenie.tools)
save_plugin_data() (snipgenie.gui.App method)
save_project() (snipgenie.gui.App method)
save_project_dialog() (snipgenie.gui.App method)
save_settings() (snipgenie.gui.App method)
set_annotation() (snipgenie.gui.App method)
set_attributes() (in module snipgenie.tools)
set_chrom() (snipgenie.widgets.GraphicalBamViewer method)
(snipgenie.widgets.SimpleBamViewer method)
set_figure() (snipgenie.widgets.PlotViewer method)
set_mask() (snipgenie.gui.App method)
set_nodesize() (in module snipgenie.trees)
set_output_folder() (snipgenie.gui.App method)
set_reference() (snipgenie.gui.App method)
set_style() (snipgenie.gui.App method)
set_tiplabels() (in module snipgenie.trees)
setColor() (snipgenie.widgets.ColorButton method)
setDataFrame() (snipgenie.widgets.TableViewer method)
setDefaults() (snipgenie.widgets.PreferencesDialog method)
setup() (snipgenie.app.WorkFlow method)
setup_gui() (snipgenie.gui.App method)
setup_paths() (snipgenie.gui.App method)
setWidgetValue() (snipgenie.widgets.BaseOptions method)
setWidgetValues() (in module snipgenie.widgets)
show_bam_viewer() (snipgenie.gui.App method)
show_blast_url() (snipgenie.gui.App method)
show_browser_tab() (snipgenie.gui.App method)
show_colors() (in module snipgenie.plotting)
show_error_log() (snipgenie.gui.App method)
show_info() (snipgenie.gui.App method)
show_map() (snipgenie.gui.App method)
show_nucldb_url() (snipgenie.gui.App method)
show_phylogeny() (snipgenie.gui.App method)
show_plugin() (snipgenie.gui.App method)
show_recent_files() (snipgenie.gui.App method)
show_records() (snipgenie.widgets.FileViewer method)
show_ref_annotation() (snipgenie.gui.App method)
show_snpdist() (snipgenie.gui.App method)
show_variants() (snipgenie.gui.App method)
showDialog() (snipgenie.widgets.BaseOptions method)
SimpleBamViewer (class in snipgenie.widgets)
site_proximity_filter() (in module snipgenie.app)
snipgenie
module
snipgenie.aligners
module
snipgenie.app
module
snipgenie.gui
module
snipgenie.plotting
module
snipgenie.simulate
module
snipgenie.tools
module
snipgenie.trees
module
snipgenie.widgets
module
snp_alignment() (snipgenie.gui.App method)
snp_dist_matrix() (in module snipgenie.tools)
snp_typing() (snipgenie.gui.App method)
snp_viewer() (snipgenie.gui.App method)
start() (snipgenie.gui.StdoutRedirect method)
start_logging() (snipgenie.gui.App method)
staticMetaObject (snipgenie.gui.App attribute)
(snipgenie.gui.Communicate attribute)
(snipgenie.gui.StdoutRedirect attribute)
(snipgenie.gui.WorkerSignals attribute)
(snipgenie.widgets.BasicDialog attribute)
(snipgenie.widgets.BrowserViewer attribute)
(snipgenie.widgets.ColorButton attribute)
(snipgenie.widgets.DynamicDialog attribute)
(snipgenie.widgets.Editor attribute)
(snipgenie.widgets.FileViewer attribute)
(snipgenie.widgets.GraphicalBamViewer attribute)
(snipgenie.widgets.MergeDialog attribute)
(snipgenie.widgets.MultipleInputDialog attribute)
(snipgenie.widgets.PlainTextEditor attribute)
(snipgenie.widgets.PlotViewer attribute)
(snipgenie.widgets.PreferencesDialog attribute)
(snipgenie.widgets.SimpleBamViewer attribute)
(snipgenie.widgets.TableViewer attribute)
(snipgenie.widgets.TextViewer attribute)
(snipgenie.widgets.ToolBar attribute)
StdoutRedirect (class in snipgenie.gui)
stop() (snipgenie.gui.StdoutRedirect method)
subread_align() (in module snipgenie.aligners)
T
TableViewer (class in snipgenie.widgets)
test_run() (in module snipgenie.app)
TextViewer (class in snipgenie.widgets)
ToolBar (class in snipgenie.widgets)
toytree_draw() (in module snipgenie.trees)
tree_viewer() (snipgenie.gui.App method)
trim_files() (in module snipgenie.app)
trim_reads() (in module snipgenie.tools)
trim_reads_default() (in module snipgenie.tools)
U
update() (snipgenie.widgets.BasicDialog method)
update_chrom() (snipgenie.widgets.GraphicalBamViewer method)
(snipgenie.widgets.SimpleBamViewer method)
update_labels() (snipgenie.gui.App method)
update_mask() (snipgenie.gui.App method)
update_plugin_menu() (snipgenie.gui.App method)
update_ref_genome() (snipgenie.gui.App method)
update_table() (snipgenie.gui.App method)
update_urlbar() (snipgenie.widgets.BrowserViewer method)
updateColumns() (snipgenie.widgets.MergeDialog method)
updateWidgets() (snipgenie.widgets.BaseOptions method)
(snipgenie.widgets.PreferencesDialog method)
V
value_changed() (snipgenie.widgets.GraphicalBamViewer method)
(snipgenie.widgets.SimpleBamViewer method)
variant_calling() (in module snipgenie.app)
(snipgenie.gui.App method)
vcf_to_dataframe() (in module snipgenie.tools)
vcf_viewer() (snipgenie.gui.App method)
W
Worker (class in snipgenie.gui)
worker() (in module snipgenie.app)
WorkerSignals (class in snipgenie.gui)
WorkFlow (class in snipgenie.app)
write() (snipgenie.app.Logger method)
(snipgenie.gui.StdoutRedirect method)
write_samples() (in module snipgenie.app)
Z
zoom() (snipgenie.widgets.BrowserViewer method)
(snipgenie.widgets.Editor method)
(snipgenie.widgets.PlainTextEditor method)
(snipgenie.widgets.PlotViewer method)
zoom_in() (snipgenie.gui.App method)
(snipgenie.widgets.GraphicalBamViewer method)
(snipgenie.widgets.SimpleBamViewer method)
zoom_out() (snipgenie.gui.App method)
(snipgenie.widgets.GraphicalBamViewer method)
(snipgenie.widgets.SimpleBamViewer method)
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