Index

_

__repr__() (FilterFilepath method) (FilterListModel method) (FilterParameter method) (FilterSwitch method) (FilterThreshold method) (Workflow method)

__str__() (FilterParameter method) (Workflow method)

A

add_filter() (MainWindow method) add_parameter() (FilterItem method) (FilterWidget method) add_recent_file() (MainWindow method)

addActions() (MainWindow method) adjust_quality() (in module pmdtools.pmdtools_mod) aln_identity() (in module samsifter.util.genetics)

B

BashOptions (class in samsifter.gui.dialogs)

BashOptionsDialog (class in samsifter.gui.dialogs)

C

calc_avg_depth() (in module samsifter.tools.filter_ref_coverage) changed (Workflow attribute) check_csv() (in module samsifter.util.arg_sanitation) check_percent() (in module samsifter.util.arg_sanitation) check_pos_float() (in module samsifter.util.arg_sanitation) check_pos_float_max1() (in module samsifter.util.arg_sanitation) check_pos_float_max100() (in module samsifter.util.arg_sanitation) check_pos_int() (in module samsifter.util.arg_sanitation) check_sam() (in module samsifter.util.arg_sanitation) clear() (Workflow method)

cli() (FilterFilepath method) (FilterParameter method) (FilterSwitch method) (FilterThreshold method) clone() (FilterFilepath method) (FilterItem method) (FilterParameter method) (FilterSwitch method) (FilterThreshold method) closeEvent() (MainWindow method) commandline() (FilterItem method) (Workflow method) complement() (in module samsifter.util.genetics) configure_bash() (MainWindow method) configure_sam2rma() (MainWindow method) covered_length_from_cigar() (in module samsifter.tools.filter_ref_coverage) create_pg_line() (in module samsifter.util.papertrail)

D

data() (FilterListModel method) decompress_cigar() (in module samsifter.util.sam) decompress_md() (in module samsifter.util.sam) delete_item() (MainWindow method)

denormalize() (SliderSpinboxCombo method) deserialize() (samsifter.util.serialize.WorkflowSerializer class method) determine_type() (samsifter.util.serialize.WorkflowSerializer class method)

E

export_bash() (MainWindow method)

F

fa_get() (in module pmdtools.pmdtools_mod) FileChooser (class in samsifter.gui.composites) FilterFilepath (class in samsifter.models.parameter) FilterItem (class in samsifter.models.filter) FilterListModel (class in samsifter.models.filter_model) FilterListView (class in samsifter.views.filterviews) FilterParameter (class in samsifter.models.parameter) FilterSwitch (class in samsifter.models.parameter)

FilterThreshold (class in samsifter.models.parameter) FilterTreeModel (class in samsifter.models.filter_model) FilterTreeWidget (class in samsifter.views.filterviews) FilterWidget (class in samsifter.gui.widgets) find_last_in_chain() (in module samsifter.util.papertrail) flags() (FilterListModel method) formats() (Workflow static method)

G

gc() (in module samsifter.util.genetics) geometric() (in module pmdtools.pmdtools_mod) get_cli_name() (FilterParameter method) get_current_index() (OptionSwitcher method) get_default() (FilterParameter method) get_description() (FilterItem method) (FilterParameter method) get_extensions() (FilterFilepath method) get_filename() (FileChooser method) (Workflow method) get_form_text() (FilterParameter method) (FilterThreshold method) get_gini_auc() (in module samsifter.tools.filter_ref_coverage) get_icon_path() (FilterItem method) get_in_filename() (Workflow method) get_input_compression() (FilterItem method) get_input_errors() (WorkflowValidator method) get_input_format() (FilterItem method) get_input_sorting() (FilterItem method) get_max_expected() (RmaOptions method) get_maximum() (FilterThreshold method) get_min_score() (RmaOptions method) get_min_support() (RmaOptions method) get_min_support_percent() (RmaOptions method) get_minimum() (FilterThreshold method)

get_model() (Workflow method) get_model_errors() (WorkflowValidator method) get_option() (FilterSwitch method) get_options() (BashOptionsDialog method) (FilterSwitch method) (OptionSwitcher method) (RmaOptionsDialog method) get_out_filename() (Workflow method) get_output_compression() (FilterItem method) get_output_errors() (WorkflowValidator method) get_output_format() (FilterItem method) get_output_sorting() (FilterItem method) get_parameters() (FilterItem method) get_precision() (FilterThreshold method) get_print_commands() (BashOptions method) get_processing_mode() (BashOptions method) get_run_compile_stats() (Workflow method) get_run_sam2rma() (Workflow method) get_sam2rma_path() (RmaOptions method) get_stop_on_error() (BashOptions method) get_suffix_string() (FileChooser method) get_top_percent() (RmaOptions method) get_unit() (FilterThreshold method) get_use_basenames() (BashOptions method) get_value() (FilterParameter method) (SliderSpinboxCombo method)

H

highlight() (FileChooser method) (InputWidget method) (OutputWidget method)

I

ICON_ANALYZER (FilterItem attribute) ICON_CONVERTER (FilterItem attribute) ICON_FILTER (FilterItem attribute) ICON_SORTER (FilterItem attribute) index() (FilterListModel method) infile_is_valid() (Workflow method) init_ui() (MainWindow method) input_changed (Workflow attribute) InputWidget (class in samsifter.gui.widgets) insertItem() (FilterListModel method)

integral_discrete() (in module samsifter.tools.filter_ref_coverage) integral_scaled() (in module samsifter.tools.filter_ref_coverage) is_active() (FilterParameter method) is_dirty() (Workflow method) is_iupac() (in module samsifter.util.genetics) is_required() (FilterParameter method) is_valid() (FilterItem method) (Workflow method) item() (in module samsifter.tools.bam_2_sam) (in module samsifter.tools.calculate_pmds) (in module samsifter.tools.compress) (in module samsifter.tools.count_taxon_reads) (in module samsifter.tools.decompress) (in module samsifter.tools.filter_read_conservation) (in module samsifter.tools.filter_read_identity) (in module samsifter.tools.filter_read_list) (in module samsifter.tools.filter_read_pmds) (in module samsifter.tools.filter_ref_coverage) (in module samsifter.tools.filter_ref_identity) (in module samsifter.tools.filter_ref_list) (in module samsifter.tools.filter_ref_pmds) (in module samsifter.tools.filter_taxon_list) (in module samsifter.tools.filter_taxon_pmds) (in module samsifter.tools.remove_duplicates) (in module samsifter.tools.sam_2_bam) (in module samsifter.tools.sort_by_coordinates) (in module samsifter.tools.sort_by_names) item_changed (FilterListModel attribute) iterate_items() (FilterListModel method) (FilterTreeModel method)

L

likelihood_match() (in module pmdtools.pmdtools_mod) likelihood_mismatch() (in module pmdtools.pmdtools_mod) line_filter() (in module samsifter.util.filters) list_changed (Workflow attribute) load() (Workflow method)

load_file() (MainWindow method) load_initial_file() (MainWindow method) lorenzify() (in module samsifter.tools.filter_ref_coverage) lorenzify_b2b() (in module samsifter.tools.filter_ref_coverage)

M

main() (in module pmdtools.pmdtools_mod) (in module samsifter.samsifter) (in module samsifter.stats.compile_stats) (in module samsifter.stats.summarize_stats) (in module samsifter.tools.count_taxon_reads) (in module samsifter.tools.filter_read_conservation) (in module samsifter.tools.filter_read_list) (in module samsifter.tools.filter_ref_coverage) (in module samsifter.tools.filter_ref_identity) (in module samsifter.tools.filter_ref_list) (in module samsifter.tools.filter_ref_pmds) (in module samsifter.tools.filter_taxon_list) (in module samsifter.tools.filter_taxon_pmds) (in module samsifter.util.filters) (in module samsifter.util.papertrail) (in module samsifter.util.sam) MainWindow (class in samsifter.samsifter) make_widget() (FilterItem method) modify_header() (in module samsifter.util.papertrail)

move_current() (MainWindow method) move_current_down() (MainWindow method) move_current_up() (MainWindow method)

N

new_file() (MainWindow method)

normalize() (SliderSpinboxCombo method)

O

ok_to_continue() (MainWindow method) on_change() (Workflow method) on_compilation_finished() (MainWindow method) on_insert() (Workflow method) on_list_item_doubleclick() (MainWindow method) on_postprocessing_finished() (MainWindow method) on_remove() (Workflow method) on_settings_change() (MainWindow method) on_slider_value_change() (SliderSpinboxCombo method) on_spinner_value_change() (SliderSpinboxCombo method) on_stderr() (MainWindow method) on_stdout() (MainWindow method)

on_stdout_stats() (MainWindow method) on_tree_item_doubleclick() (MainWindow method) on_validity_change() (MainWindow method) on_value_change() (FilterWidget method) on_workflow_finished() (MainWindow method) open_file() (MainWindow method) opposite() (in module samsifter.util.genetics) OptionSwitcher (class in samsifter.gui.composites) outfile_is_valid() (Workflow method) output_changed (Workflow attribute) OutputWidget (class in samsifter.gui.widgets)

P

PARALLEL_MODE (BashOptions attribute) pattern_filter() (in module samsifter.util.filters) phred2prob() (in module pmdtools.pmdtools_mod) plot_ccd() (in module samsifter.tools.filter_ref_coverage) plot_cd() (in module samsifter.tools.filter_ref_coverage) plot_lorenz() (in module samsifter.tools.filter_ref_coverage) plot_lorenz_b2b() (in module samsifter.tools.filter_ref_coverage) plot_nccd() (in module samsifter.tools.filter_ref_coverage) plot_rld() (in module samsifter.tools.filter_ref_coverage) plot_sccd() (in module samsifter.tools.filter_ref_coverage) plot_scd() (in module samsifter.tools.filter_ref_coverage) pmdtools (module)

pmdtools.pmdtools_mod (module) populate_file_menu() (MainWindow method) populate_filter_menu() (MainWindow method) populate_filters() (MainWindow method) prettify() (samsifter.util.serialize.WorkflowSerializer class method) print_command() (MainWindow method) print_wf() (MainWindow method) print_xml() (MainWindow method) prob() (in module pmdtools.pmdtools_mod) prob2ascii() (in module pmdtools.pmdtools_mod) prob2phred() (in module pmdtools.pmdtools_mod)

R

reconstruct() (in module samsifter.util.sam) removeAll() (FilterListModel method) removeRow() (FilterListModel method) removeRows() (FilterListModel method) reset_form() (RmaOptionsDialog method) reverse() (in module samsifter.util.genetics) reverse_complement() (in module samsifter.util.genetics)

reverse_transcribe() (in module samsifter.util.genetics) RmaOptions (class in samsifter.gui.dialogs) RmaOptionsDialog (class in samsifter.gui.dialogs) rowCount() (FilterListModel method) run_compile_stats_command() (MainWindow method) run_sam2rma_command() (MainWindow method) run_workflow_command() (MainWindow method)

S

samsifter (module) samsifter.gui (module) samsifter.gui.composites (module) samsifter.gui.dialogs (module) samsifter.gui.widgets (module) samsifter.models (module) samsifter.models.filter (module) samsifter.models.filter_model (module) samsifter.models.parameter (module) samsifter.models.workflow (module) samsifter.resources (module) samsifter.samsifter (module) samsifter.stats (module) samsifter.stats.compile_stats (module) samsifter.stats.summarize_stats (module) samsifter.tools (module) samsifter.tools.bam_2_sam (module) samsifter.tools.calculate_pmds (module) samsifter.tools.compress (module) samsifter.tools.count_taxon_reads (module) samsifter.tools.decompress (module) samsifter.tools.filter_read_conservation (module) samsifter.tools.filter_read_identity (module) samsifter.tools.filter_read_list (module) samsifter.tools.filter_read_pmds (module) samsifter.tools.filter_ref_coverage (module) samsifter.tools.filter_ref_identity (module) samsifter.tools.filter_ref_list (module) samsifter.tools.filter_ref_pmds (module) samsifter.tools.filter_taxon_list (module) samsifter.tools.filter_taxon_pmds (module) samsifter.tools.remove_duplicates (module) samsifter.tools.sam_2_bam (module) samsifter.tools.sort_by_coordinates (module) samsifter.tools.sort_by_names (module) samsifter.util (module) samsifter.util.arg_sanitation (module) samsifter.util.filters (module) samsifter.util.genetics (module) samsifter.util.papertrail (module) samsifter.util.sam (module) samsifter.util.serialize (module) samsifter.util.validation (module) samsifter.version (module) samsifter.views (module) samsifter.views.filterviews (module) save() (Workflow method) save_file() (MainWindow method) save_file_as() (MainWindow method) save_options() (BashOptionsDialog method) (RmaOptionsDialog method) save_xml() (Workflow method) score_pmd() (in module pmdtools.pmdtools_mod) SEQUENTIAL_MODE (BashOptions attribute)

serialize() (samsifter.util.serialize.WorkflowSerializer class method) set_active() (FilterParameter method) set_cli_name() (FilterParameter method) set_command() (FilterItem method) set_current_index() (OptionSwitcher method) set_default() (FilterParameter method) set_description() (FilterItem method) (FilterParameter method) set_dirty() (Workflow method) set_extensions() (FilterFilepath method) set_filename() (FileChooser method) (InputWidget method) (OutputWidget method) (Workflow method) set_icon_path() (FilterItem method) set_in_filename() (Workflow method) set_infile_valid() (Workflow method) set_input_compression() (FilterItem method) set_input_format() (FilterItem method) set_input_sorting() (FilterItem method) set_max_expected() (RmaOptions method) set_maximum() (FilterThreshold method) set_min_score() (RmaOptions method) set_min_support() (RmaOptions method) set_min_support_percent() (RmaOptions method) set_minimum() (FilterThreshold method) set_options() (FilterSwitch method) (OptionSwitcher method) set_out_filename() (Workflow method) set_outfile_valid() (Workflow method) set_output_compression() (FilterItem method) set_output_format() (FilterItem method) set_output_sorting() (FilterItem method) set_precision() (FilterThreshold method) set_print_commands() (BashOptions method) set_processing_mode() (BashOptions method) set_required() (FilterParameter method) set_run_compile_stats() (Workflow method) set_run_sam2rma() (Workflow method) set_sam2rma_path() (RmaOptions method) set_stop_on_error() (BashOptions method) set_suffix_string() (FileChooser method) set_top_percent() (RmaOptions method) set_unit() (FilterThreshold method) set_use_basenames() (BashOptions method) set_valid() (FilterItem method) (Workflow method) set_value() (FilterFilepath method) (FilterParameter method) (FilterSwitch method) (FilterThreshold method) (SliderSpinboxCombo method) show_about() (MainWindow method) show_dialog() (FileChooser method) (InputWidget method) (OutputWidget method) show_help() (MainWindow method) sigint_handler() (in module samsifter.samsifter) SINGLE_MODE (BashOptions attribute) singletons() (samsifter.util.serialize.WorkflowSerializer class method) SliderSpinboxCombo (class in samsifter.gui.composites) stop_command() (MainWindow method) supportedDragActions() (FilterListModel method) (FilterTreeModel method) supportedDropActions() (FilterListModel method)

T

takeItem() (FilterListModel method) test_deletion_snp_0_delim() (in module samsifter.util.sam) test_deletion_snp_no_delim() (in module samsifter.util.sam) test_hard_clipping_end() (in module samsifter.util.sam) test_hard_clipping_front() (in module samsifter.util.sam) test_insertion() (in module samsifter.util.sam) test_skipped_intron() (in module samsifter.util.sam) test_soft_clipping_end() (in module samsifter.util.sam)

test_soft_clipping_front() (in module samsifter.util.sam) to_bash() (Workflow method) to_xml_string() (Workflow method) transcribe() (in module samsifter.util.genetics) tree_from_file() (samsifter.util.serialize.WorkflowSerializer class method) tree_to_file() (samsifter.util.serialize.WorkflowSerializer class method) tree_to_str() (samsifter.util.serialize.WorkflowSerializer class method)

U

update_settings_view() (MainWindow method)

update_status() (MainWindow method)

V

validate() (WorkflowValidator method) validate_input() (WorkflowValidator method) validate_model() (WorkflowValidator method) validate_output() (WorkflowValidator method)

validate_wf() (MainWindow method) validity_changed (Workflow attribute) value_changed (FilterWidget attribute)

W

Workflow (class in samsifter.models.workflow) workflow_from_xml() (samsifter.util.serialize.WorkflowSerializer class method) workflow_to_xml() (samsifter.util.serialize.WorkflowSerializer class method)

WorkflowSerializer (class in samsifter.util.serialize) WorkflowValidator (class in samsifter.util.validation)