Command line API reference

Below is the technical documentation for Smoother’s command line interface.

usage: biosmoother [-h] [-v]
                   {serve,init,reset,repl,cool,track,export,set,get,par_info,test,benchmark,ploidy}
                   ...

Positional Arguments

cmd

Possible choices: serve, init, reset, repl, cool, track, export, set, get, par_info, test, benchmark, ploidy

Sub-command that shall be executed.

Named Arguments

-v, --version: Print Smoother’s version and exit.

Sub-commands

serve

Open Smoother’s graphical user interface and launch an exisiting existing index. If an index has been already launched before, the session will be restored with the parameters of the last session.

biosmoother serve [-h] [-s] [-k] [-q] [--port PORT] [--address ADDRESS]
                  [--show] [--allow-websocket-origin HOST[:PORT]]
                  index_prefix

Positional Arguments

index_prefix: Path to the index directory generated with the init command.

Named Arguments

-s, --no_save: Disable saving changes to the current session. This is intended for hosting public datasets (default: off)
-k, --keep_alive: Keep Smoother alive when it’s browser tab is closed. Smoother then can be reopened from the link without re-running the serve command. (default: off)
-q, --quiet: Print less information about the ongoing processes on the command line. (default: off)
--port: Use a particular port.
--address: Use a particular address.
--show: Immediateley open a browser tab for the served index. Only works if run locally.
--allow-websocket-origin: Public hostnames which may connect to the Smoother server. Check https://docs.bokeh.org/en/latest/docs/user_guide/server/deploy.html#security for more details.

init

Either –anno_path or –ctg_len must be given.

biosmoother init [-h] [-c [CTG_LEN]] [-a [ANNO_PATH]]
                 [-f [FILTERABLE_ANNOTATIONS ...]] [-m [MAP_Q_THRESHOLDS ...]]
                 [-d DIVIDEND] [--ploidy_file PLOIDY_FILE]
                 index_prefix

Positional Arguments

index_prefix: Path where the index directory will be saved. Note: a folder with multiple files will be created.

Named Arguments

-c, --ctg_len: Path to a 2-column tab separated file containing the contig names and their size in basepairs. The order of contigs in this file will determine the order they are displayed in. If no –anno_path is given, this parameter becomes required.
-a, --anno_path: Path to a GFF file containing the annotations of the reference genome. If –ctg_len is not given this parameter becomes required and the order of contigs will be inferred from the order of ‘##sequence-region’ lines in this GFF file.
-f, --filterable_annotations: List the annotations that can be used as filters. The annotations listed must be present in the ‘anno_path’ GFF file. (default: gene)
-m, --map_q_thresholds: List several thresholds that can be used to filter reads by mapping quality score. (default: 3 30)
-d, --dividend: Divide all coordinates by this number, this corresponds to the minimal bin size that can be displayed. Larger numbers will reduce the index size and pre-processing time. (default: 10000)
--ploidy_file: File that specifies the ploidy for each chromosome.

reset

Reset a given index with to the default parameters.

biosmoother reset [-h] index_prefix

Positional Arguments

index_prefix: Path to the index directory generated with the init command.

repl

Add data for a sample or replicate to an index.

The detailed explanation for the input format can be found here.

biosmoother repl [-h] [-g {a,b,both,neither}] [-q] [-m] [-a] [-s]
                 [-C [COLUMNS ...]] [-u]
                 index_prefix path name

Positional Arguments

index_prefix: Path to the index directory generated with the init command.
path: Path to the input pairs file containing the interactions.
name: Name for the new replicate or sample.

Named Arguments

-g, --group

Possible choices: a, b, both, neither

Analysis group or condition for the new replicate. This can also be modified in the GUI. Options are: ‘a’, ‘b’, ‘both’, ‘neither’. (default: “a”)

-q, --no_map_q

Do not store mapping quality information for the replicate/sample. This will make the index smaller. (default: off)

-m, --no_multi_map

Exclude multi mapping reads from the analysis. For reads mapping to multiple loci only the main mapping position will be kept, and the secondary alignments will be ignored. This will make the index smaller. Note that if multiple alignments are not marked as one primary and other secondary alignments (I.e., they are kept in different lines in the input pairs file), only the first line with a given readID will be kept (default: off)

-a, --no_anno

Do not store annotation information. (default: off)

-s, --strand

Do store strand information. (default: off)

-C, --columns

Define the order of columns of the input pairs file. Valid column names are: ‘readId’, ‘chr1’, ‘chr2’, ‘pos1’, ‘pos2’, ‘strand1’, ‘strand2’, ‘mapq1’, ‘mapq2’, ‘xa1’, ‘xa2’, ‘cnt’, ‘pair_type’, and ‘.’. Specify the columns as a space separated list: ‘-C chr1 pos1 [xa1]’. Column names in squared brackets indicate optional columns (e.g. ‘[mapq1] [mapq2]’). Optional columns must not appear in all lines of the input file. ‘chr1’, ‘chr2’, ‘pos1’ and ‘pos2’ must be defined and cannot be optional columns. If a row in the input file has less columns than defined, optional columns will be ignored starting from the end. If a row in the input file contains more than the given columns, the superfluous columns will be ignored starting from the end. Columns defined as ‘.’ or ‘[.]’ will be ignored. Lines in the input file that start with ‘#columns:’ will set this parameter for all following lines, if the parameter has not been specified on the command line. (default: [readID] chr1 pos1 chr2 pos2 [strand1] [strand2] [.] [mapq1] [mapq2] [xa1] [xa2] [cnt])

-u, --force_upper_triangle

Move all interactions to the upper triangle and keep the lower triangle empty. Enable this option for symmetric data (e.g., Hi-C) with a non-redundant and non-sorted input pairs file. If the input file has sorted pairs, or the data is asymmetric (e.g., RD-SPRITE) this option is not needed. (default: off)

cool

Add data for a sample or replicate to an index from a cooler file. Note: The information necessary to apply filters (e.g. the mapping quality of reads) is not stored in cool files, therefore filters will be disabled for datasets created from cool files.

biosmoother cool [-h] [-g {a,b,both,neither}] [-a] [-u] index_prefix path name

Positional Arguments

index_prefix: Path to the index directory generated with the init command.
path: Path to the input pairs file containing the interactions.
name: Name for the new replicate or sample.

Named Arguments

-g, --group

Possible choices: a, b, both, neither

Analysis group or condition for the new replicate. This can also be modified in the GUI. Options are: ‘a’, ‘b’, ‘both’, ‘neither’. (default: “a”)

-a, --no_anno

Do not store annotation information. (default: off)

-u, --force_upper_triangle

Move all interactions to the upper triangle and keep the lower triangle empty. Enable this option for symmetric data (e.g., Hi-C) with a non-redundant and non-sorted input pairs file. If the input file has sorted pairs, or the data is asymmetric (e.g., RD-SPRITE) this option is not needed. (default: off)

track

Add a track of uni-dimensional sequencing data that can be used for normalisation on Smoother to an index.

The detailed explanation for the input format can be found here.

biosmoother track [-h] [-x {row,col,both,neither}] [-q] [-m] [-a] [-s]
                  [-C [COLUMNS ...]]
                  index_prefix path name

Positional Arguments

index_prefix: Prefix that was used to create the index (see the init subcommand).
path: Path to the file that contains the aligned reads.
name: Name for the new normalization track.

Named Arguments

-x, --axis

Possible choices: row, col, both, neither

Axis in which the uni-dimensional track will be displayed. This can also be modified interactively. Options are: ‘row’, ‘col’, ‘both’, ‘neither’ (default: “neither”)

-q, --no_map_q

Do not store mapping quality information for the replicate/sample. This will make the index smaller. (default: off)

-m, --no_multi_map

Exclude multi mapping reads from the analysis. For reads mapping to multiple loci only the main mapping position will be kept, and all secondary alignments will be ignored. This will make the index smaller. Note that if multiple alignments are not marked as one primary and other secondary alignments and are thus kept in different lines in the input pairs file, only the first line with a given readID will be kept. (default: off)

-a, --no_anno

Do not store annotation information. This will make the index smaller. (default: off)

-s, --strand

Do store strand information. This will make the index larger. (default: off)

-C, --columns

Define the order of columns of the input file. Valid column names are: ‘readId’, ‘chr’, ‘pos’, ‘strand’, ‘mapq’, ‘xa’, ‘cnt’, and ‘.’. Specify the columns as a space separated list: ‘-C chr pos [xa]’. Column names in squared brackets indicate optional columns (e.g. ‘[mapq] [xa]’). Optional columns must not appear in all lines of the input file. ‘chr’ and ‘pos’ must be defined and cannot be optional columns. If a row in the input file has less columns than defined, optional columns will be ignored starting from the end. If a row in the input file contains more than the given columns, the superfluous columns will be ignored starting from the end. Columns defined as ‘.’ or ‘[.]’ will be ignored. Lines in the input file that start with ‘#columns:’ will set this parameter for all following lines, if the parameter has not been specified on the command line. (default: [readID] chr pos [strand] [mapq] [xa] [cnt])

export

Export the current index session to a file.

biosmoother export [-h] [-p EXPORT_PREFIX] [-f [{tsv,svg,png} ...]]
                   [-s EXPORT_SIZE]
                   index_prefix

Positional Arguments

index_prefix: Path to the index directory generated with the init command.

Named Arguments

-p, --export_prefix

Path for the exported files. The appropriate file extension will be added automatically.

-f, --export_format

Possible choices: tsv, svg, png

File format to be exported. Format options are ‘tsv’, ‘svg’, ‘png’. When exporting in tsv format, 3 files are saved: one for the interactome, and one for each axis. Multiple formats can be exported at once: For example, using the argument ‘-f tsv png’ will export both the tsv text file and a png picture. (Default: tsv)

-s, --export_size

Size in pixels of the heatmap. (default: 800)

set

Set the values of different parameters in an index. This can also be done on in the graphical user interface.

A list of parameters can be found here.

biosmoother set [-h] index_prefix name val

Positional Arguments

index_prefix: Path to the index directory generated with the init command.
name: The name of the parameter to set. The parameter names can be found in the manual https://biosmoother.readthedocs.io
val: The value to set.

get

Retrieve the value of a parameter from the current session of an index. This can also be done on in the graphical user interface.

A list of parameters can be found here.

biosmoother get [-h] index_prefix name

Positional Arguments

index_prefix: Path to the index directory generated with the init command.
name: The name of the parameter to get. The parameter names can be found in the manual https://biosmoother.readthedocs.io. If a ‘.’ is given for the name argument, the whole session will be printed. If ‘settings’ is given for the name argument, all settings will be printed.

par_info

Undocumented

biosmoother par_info [-h] [-n NAME] index_prefix

Positional Arguments

index_prefix: Prefix that was used to create the index (see the init subcommand).

Named Arguments

-n, --name: The name of the parameter to get.

test

Undocumented

biosmoother test [-h] [-S SEED] [-s SKIP_FIRST] index_prefix

Positional Arguments

index_prefix: Path to the index directory generated with the init command.

Named Arguments

-S, --seed: Seed for random configurations.
-s, --skip_first: Skip the first x many test

benchmark

Undocumented

biosmoother benchmark [-h] [-N NUM_EXPERIMENTS] [-o OUTFILE] index_prefix

Positional Arguments

index_prefix: Path to the index directory generated with the init command.

Named Arguments

-N, --num_experiments: Number of samples to take. (default: 100)
-o, --outfile: outputfile

ploidy

Add a ploidy file to the index.

biosmoother ploidy [-h] index_prefix ploidy_file

Positional Arguments

index_prefix: Path to the index directory generated with the init command.
ploidy_file: File that specifies the ploidy for each contig. The format of this file is described in the manual: https://biosmoother.rtdf.io

Index Parameters

Below is a list of all parameters that can be changed in an index session. This changing can be done using the set and get commands or via the graphical user interface.

The Annotation group

filter_absent_x

Full parameter name: annotation.filter_absent_x
Description: Apply the annotation filter to the columns. Then only interactions that overlap the picked annotation on the x-axis are displayed.

Accepted values: [], [annotation_a], [annotation_a, annotation_b, ...]
Value type: list
Button in GUI: Filter->Annotations Filter out interactions that don’t overlap annotation (see in manual)

filter_absent_y

Full parameter name: annotation.filter_absent_y
Description: Apply the annotation filter to the rows. Then only interactions that overlap the picked annotation on the y-axis are displayed.

Accepted values: [], [annotation_a], [annotation_a, annotation_b, ...]
Value type: list
Button in GUI: Filter->Annotations Filter out interactions that don’t overlap annotation (see in manual)

filter_present_x

Full parameter name: annotation.filter_present_x
Description: Apply the annotation filter to the columns. Then only interactions that do not overlap the picked annotation on the x-axis are displayed.

Accepted values: [], [annotation_a], [annotation_a, annotation_b, ...]
Value type: list
Button in GUI: Filter->Annotations Filter out interactions that overlap annotation (see in manual)

filter_present_y

Full parameter name: annotation.filter_present_y
Description: Apply the annotation filter to the rows. Then only interactions that do not overlap the picked annotation on the y-axis are displayed.

Accepted values: [], [annotation_a], [annotation_a, annotation_b, ...]
Value type: list
Button in GUI: Filter->Annotations Filter out interactions that overlap annotation (see in manual)

visible_x

Full parameter name: annotation.visible_x
Description: Pick which annotations to display.

Accepted values: [], [annotation_a], [annotation_a, annotation_b, ...]
Value type: list
Button in GUI: Filter->Annotations Visible Annotations (see in manual)

visible_y

Full parameter name: annotation.visible_y
Description: Pick which annotations to display.

Accepted values: [], [annotation_a], [annotation_a, annotation_b, ...]
Value type: list
Button in GUI: Filter->Annotations Visible Annotations (see in manual)

area

Full parameter name: area
Description: Area that is displayed in the heatmap.

Accepted values: text in the navigation syntax (see the ‘The Navigation bar’ chaper in the manual).
Value type: string
Button in GUI: Navigation Bar (see in manual)

The Contigs group

annotation_coordinates

Full parameter name: contigs.annotation_coordinates
Description: Pick the annotation used for the annotation coordinate system

Accepted values: annotation_a, annotation_b, annotation_c, ...
Value type: string
Button in GUI: Filter->Coordinates Annotation Coordinate System (see in manual)

displayed_on_x

Full parameter name: contigs.displayed_on_x
Description: Pick which contigs to display.

Accepted values: [], [contig_a], [contig_a, contig_b, ...]
Value type: list
Button in GUI: Filter->Coordinates Active Contigs (see in manual)

displayed_on_x_ploidy

Full parameter name: contigs.displayed_on_x_ploidy
Description: Pick which contigs to display.

Accepted values: [], [contig_a], [contig_a, contig_b, ...]
Value type: list
Button in GUI: Filter->Coordinates Active Contigs (see in manual)

displayed_on_y

Full parameter name: contigs.displayed_on_y
Description: Pick which contigs to display.

Accepted values: [], [contig_a], [contig_a, contig_b, ...]
Value type: list
Button in GUI: Filter->Coordinates Active Contigs (see in manual)

displayed_on_y_ploidy

Full parameter name: contigs.displayed_on_y_ploidy
Description: Pick which contigs to display.

Accepted values: [], [contig_a], [contig_a, contig_b, ...]
Value type: list
Button in GUI: Filter->Coordinates Active Contigs (see in manual)

The Coverage group

in_column

Full parameter name: coverage.in_column
Description: pick which tracks to display on the x/y-axis and to include in the main coverage

Accepted values: [], [sec_dataset_a], [sec_dataset_a, sec_dataset_b, ...]
Value type: list
Button in GUI: Filter->Datapools Secondary Datapools (see in manual)

in_row

Full parameter name: coverage.in_row
Description: pick which tracks to display on the x/y-axis and to include in the main coverage

Accepted values: [], [sec_dataset_a], [sec_dataset_a, sec_dataset_b, ...]
Value type: list
Button in GUI: Filter->Datapools Secondary Datapools (see in manual)

The Replicates group

in_group_a

Full parameter name: replicates.in_group_a
Description: options for combining the individual datasets

Accepted values: [], [dataset_a], [dataset_a, dataset_b, ...]
Value type: list
Button in GUI: Filter->Datapools Primary Datapools (see in manual)

in_group_b

Full parameter name: replicates.in_group_b
Description: options for combining the individual datasets

Accepted values: [], [dataset_a], [dataset_a, dataset_b, ...]
Value type: list
Button in GUI: Filter->Datapools Primary Datapools (see in manual)

The Settings group

The Export subgroup

axis

Full parameter name: settings.export.axis.val
Description: The size of the area the secondary axes are rendered in for the exported image.

Accepted values: 0 .. 2000
Value type: integer
Default value: 125
Button in GUI: File->Export Secondary Axis size (see in manual)

contigs

Full parameter name: settings.export.contigs.val
Description: The size of the area contig names are rendered in for the exported image.

Accepted values: 0 .. 2000
Value type: integer
Default value: 125
Button in GUI: File->Export Contig size (see in manual)

coords

Full parameter name: settings.export.coords.val
Description: The size of the area coordinates are rendered in for the exported image.

Accepted values: 0 .. 2000
Value type: integer
Default value: 125
Button in GUI: File->Export Coordinate size (see in manual)

do_export_full

Full parameter name: settings.export.do_export_full
Description: Export the full matrix instead of merely the visible area.

Accepted values: True, False
Value type: boolean
Default value: False
Button in GUI: File->Export Export full matrix instead of visible region (see in manual)

export_format

Full parameter name: settings.export.export_format
Description: Pick the format that files shall be exported to.

Accepted values: tsv, png, svg
Value type: string
Default value: tsv
Button in GUI: File->Export Format (see in manual)

export_to_server

Full parameter name: settings.export.export_to_server
Description: Export files to the server instead of downloading them.

Accepted values: True, False
Value type: boolean
Default value: False
Button in GUI: File->Export Export files to server instead of downloading them (see in manual)

margins

Full parameter name: settings.export.margins.val
Description: The margins between panels when exporting to a PNG or SVG picture file.

Accepted values: 0 .. 100
Value type: integer
Default value: 10
This parameter has no button in the GUI

prefix

Full parameter name: settings.export.prefix
Description: A common prefix for exported files.

Accepted values: path/to/file
Value type: string
Default value: export
Button in GUI: File->Export Output Prefix (see in manual)

print_region

Full parameter name: settings.export.print_region
Description: Print the coordinates of the visible area (content of the navigation bar) on the top of the exported image.

Accepted values: True, False
Value type: boolean
Default value: True
This parameter has no button in the GUI

secondary_stroke_width

Full parameter name: settings.export.secondary_stroke_width.val
Description: For the secondary data panel: set the stroke width of lines in the exported image.

Accepted values: 1 .. 50
Value type: integer
Default value: 2
Button in GUI: File->Export Secondary Stroke Width (see in manual)

secondary_x_range

Full parameter name: settings.export.secondary_x_range.val_min and settings.export.secondary_x_range.val_max
Description: The visible axis range of the secondary data panel on the x-axis.

Accepted values: 0 .. 100
Value type: float
Default value: 0.0 and 0.0
This parameter has no button in the GUI

secondary_y_range

Full parameter name: settings.export.secondary_y_range.val_min and settings.export.secondary_y_range.val_max
Description: The visible axis range of the secondary data panel on the y-axis.

Accepted values: 0 .. 100
Value type: float
Default value: 0.0 and 0.0
This parameter has no button in the GUI

size

Full parameter name: settings.export.size.val
Description: The size of the heatmap panel in the exported image.

Accepted values: 10 .. 5000
Value type: integer
Default value: 800
This parameter has no button in the GUI

spacing

Full parameter name: settings.export.spacing.val
Description: The spacing between some panels when exporting to a PNG or SVG picture file.

Accepted values: 1 .. 100
Value type: integer
Default value: 3
This parameter has no button in the GUI

white_background

Full parameter name: settings.export.white_background
Description: Draw a white background when exporting to a PNG or SVG picture file.

Accepted values: True, False
Value type: boolean
Default value: True
This parameter has no button in the GUI

The Filters subgroup

ambiguous_mapping

Full parameter name: settings.filters.ambiguous_mapping
Description: how to deal with reads that map to more than one loci

Accepted values: enclosed, overlaps, first, last
Value type: string
Default value: enclosed
Button in GUI: Filter->Mapping Multi-Mapping reads (MMR) (see in manual)

anno_coords_col

Full parameter name: settings.filters.anno_coords_col
Description: Use annotation coordinates for the columns of the heatmap. Then, each column corresponds to a gene.

Accepted values: True, False
Value type: boolean
Default value: False
Button in GUI: Filter->Coordinates Use Annotation Coordinates for the columns (see in manual)

anno_coords_row

Full parameter name: settings.filters.anno_coords_row
Description: Use annotation coordinates for the rows of the heatmap. Then, each row corresponds to a gene.

Accepted values: True, False
Value type: boolean
Default value: False
Button in GUI: Filter->Coordinates Use Annotation Coordinates for the rows (see in manual)

anno_in_multiple_bins

Full parameter name: settings.filters.anno_in_multiple_bins
Description: For annotation-based coordinate systems: pick how to deal with annotations that fall into multiple bins.

Accepted values: stretch, separate, squeeze
Value type: string
Default value: stretch
Button in GUI: Filter->Coordinates Multiple Bins for Annotation (see in manual)

cut_off_bin

Full parameter name: settings.filters.cut_off_bin
Description: Remainder bins are the last bins in each contig. They are not fullsize, since usually the contig size is not an exact multiple of the bin size. Choose here how to deal with these bins.

Accepted values: larger, skip, smaller, fit_chrom_smaller, fit_chrom_larger, cover_multiple
Value type: string
Default value: larger
Button in GUI: View->Bins Remainder Bin (see in manual)

directionality

Full parameter name: settings.filters.directionality
Description: Filter interactions by directionality.

Accepted values: all, same, oppo, forw, rev
Value type: string
Default value: all
Button in GUI: Filter->Mapping Directionality (see in manual)

incomplete_alignments

Full parameter name: settings.filters.incomplete_alignments
Description: Some reads map to more loci on the genome than can be reported by the aligner. In this situation the aligner may choose some strategy to report at least one of the mapping loci. We call these alignments incomplete, they can be shown using this option but may introduce a lot of noise into the heatmap.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: Filter->Mapping Show multimapping reads with incomplete mapping loci lists (see in manual)

val_max

Full parameter name: settings.filters.mapping_q.val_max
Description: Filter out all reads with a mapping quality that does not fall into these bounds. The mapping quality represents an aligners confidence into the correctess of an alignment. The highest possible confidence is 254 while the lowest is zero.

Accepted values: 0, 1, 2, 3, …
Value type: integer
Default value: 254
Button in GUI: Filter->Mapping Mapping Quality: Upper Bound (see in manual)

val_min

Full parameter name: settings.filters.mapping_q.val_min
Description: Filter out all reads with a mapping quality that does not fall into these bounds. The mapping quality represents an aligners confidence into the correctess of an alignment. The highest possible confidence is 254 while the lowest is zero.

Accepted values: 0, 1, 2, 3, …
Value type: integer
Default value: 0
Button in GUI: Filter->Mapping Mapping Quality: Lower Bound (see in manual)

min_diag_dist

Full parameter name: settings.filters.min_diag_dist.val
Description: Filter out all bins closer to the diagonal than this value.

Accepted values: 0 .. 1000
Value type: integer
Default value: 0
Button in GUI: Filter->Coordinates Minimum Distance from Diagonal [kbp] (see in manual)

multiple_annos_in_bin

Full parameter name: settings.filters.multiple_annos_in_bin
Description: For annotation-based coordinate systems: pick how to deal with bins that encompass multiple annotations

Accepted values: combine, first, max_fac_pow_two, force_separate
Value type: string
Default value: combine
Button in GUI: Filter->Coordinates Multiple Annotations in Bin (see in manual)

show_contig_smaller_than_bin

Full parameter name: settings.filters.show_contig_smaller_than_bin
Description: Place a bin in contigs that are smaller than the bin-size. With many small contigs, this might slow down smoother significantly.

Accepted values: True, False
Value type: boolean
Default value: False
Button in GUI: View->Bins Fill contigs that are smaller than one bin (see in manual)

symmetry

Full parameter name: settings.filters.symmetry
Description: filter interactions for symmetry

Accepted values: all, sym, asym, mirror
Value type: string
Default value: all
Button in GUI: Filter->Coordinates Symmetry (see in manual)

The Interface subgroup

add_draw_area

Full parameter name: settings.interface.add_draw_area.val
Description: Increase the rendered area by x% over the visible area. This way, panning does not trigger re-rendering immediately.

Accepted values: 10 .. 500
Value type: integer
Default value: 20
Button in GUI: View->Rendering Additional Draw Area [%] (see in manual)

anno_size

Full parameter name: settings.interface.anno_size.val
Description: Size of the annotation plot.

Accepted values: 10 .. 500
Value type: integer
Default value: 50
Button in GUI: View->Panels Annotation panel Size [pixel] (see in manual)

axis_label_max_char

Full parameter name: settings.interface.axis_label_max_char.val
Description: Truncate labels to this many characters.

Accepted values: 1 .. 100
Value type: integer
Default value: 10
Button in GUI: View->Panels Maximal Character of Labels (see in manual)

axis_lables

Full parameter name: settings.interface.axis_lables
Description: The axis lables to display.

Accepted values: DNA_RNA, RNA_DNA, DNA_DNA, RNA_RNA
Value type: string
Default value: DNA_RNA
Button in GUI: View->Panels Axes Labels (see in manual)

center_tracks_on_bins

Full parameter name: settings.interface.center_tracks_on_bins
Description: For the secondary data panel: place the points of the line at the center of bins. If this is disabled, two line-points are drawn for every bin, one at the start one at the end.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: View->Panels Center Tracks on Bins (see in manual)

color_high

Full parameter name: settings.interface.color_high
Description: The end color of the ‘Low to High’ palette.

Accepted values: color in hex notation (e.g. #000000)
Value type: string
Default value: #ffffff
Button in GUI: View->Color Color High (see in manual)

color_low

Full parameter name: settings.interface.color_low
Description: The start color of the ‘Low to High’ palette.

Accepted values: color in hex notation (e.g. #000000)
Value type: string
Default value: #000000
Button in GUI: View->Color Color Low (see in manual)

color_palette

Full parameter name: settings.interface.color_palette
Description: Pick the color palette for the heatmap.

Accepted values: Viridis256, Plasma256, Turbo256, Fall, LowToHigh
Value type: string
Default value: Viridis256
Button in GUI: View->Color Color Palette (see in manual)

connect_tracks_over_contig_borders

Full parameter name: settings.interface.connect_tracks_over_contig_borders
Description: For the secondary data panel: connect the lines over contig borders.

Accepted values: True, False
Value type: boolean
Default value: False
Button in GUI: View->Panels Connect Tracks over Contig Borders (see in manual)

do_redraw

Full parameter name: settings.interface.do_redraw
Description: Automatically redraw the heatmap when panning or zooming.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: View->Rendering Auto Render (see in manual)

fixed_bin_size

Full parameter name: settings.interface.fixed_bin_size
Description: Use ‘fixed_bin_size_x’ and ‘fixed_bin_size_y’ as the width and height of bins in the main heatmap instead of computing the binsize from the size of the visible area.

Accepted values: True, False
Value type: boolean
Default value: False
This parameter has no button in the GUI

fixed_bin_size_x

Full parameter name: settings.interface.fixed_bin_size_x.val
Description: Use this as the width of bins in the main heatmap instead of computing the binsize from the size of the visible area.

Accepted values: 1 .. 10000
Value type: integer
Default value: 100
This parameter has no button in the GUI

fixed_bin_size_y

Full parameter name: settings.interface.fixed_bin_size_y.val
Description: Use this as the height of bins in the main heatmap instead of computing the binsize from the size of the visible area.

Accepted values: 1 .. 10000
Value type: integer
Default value: 100
This parameter has no button in the GUI

fixed_num_bins_x

Full parameter name: settings.interface.fixed_num_bins_x.val
Description: Use this as the number of bins in a row of the main heatmap instead of computing the binsize from the size of the visible area.

Accepted values: 0 .. 10000
Value type: integer
Default value: 256
This parameter has no button in the GUI

fixed_num_bins_y

Full parameter name: settings.interface.fixed_num_bins_y.val
Description: Use this as the number of bins in a column of the main heatmap instead of computing the binsize from the size of the visible area.

Accepted values: 0 .. 10000
Value type: integer
Default value: 256
This parameter has no button in the GUI

fixed_number_of_bins

Full parameter name: settings.interface.fixed_number_of_bins
Description: Use ‘fixed_number_of_bins_x’ and ‘fixed_number_of_bins_y’ as the number of bins in a row and column of the main heatmap instead of computing the binsize from the size of the visible area.

Accepted values: True, False
Value type: boolean
Default value: False
This parameter has no button in the GUI

max_detailed_anno_display

Full parameter name: settings.interface.max_detailed_anno_display
Description: If there are more annotations than X, display bins that contain an annotation instead of displaying the individual annotations.

Accepted values: 0, 1, 2, 3, …
Value type: integer
Default value: 1000
This parameter has no button in the GUI

max_num_bins

Full parameter name: settings.interface.max_num_bins.val
Description: Number of bins to display on the heatmap. This is the main runtime deciding factor.

Accepted values: 10 .. 1000
Value type: integer
Default value: 50
Button in GUI: View->Bins Max number of Bins [in thousands] (see in manual)

max_num_bins_factor

Full parameter name: settings.interface.max_num_bins_factor
Description: Factor multiplied to settings.interface.max_num_bins.

Accepted values: 0, 1, 2, 3, …
Value type: integer
Default value: 1000
This parameter has no button in the GUI

max_undo

Full parameter name: settings.interface.max_undo.val
Description: The maximum number of undo steps to keep in memory.

Accepted values: 0 .. 100
Value type: integer
Default value: 25
This parameter has no button in the GUI

min_bin_size

Full parameter name: settings.interface.min_bin_size.val
Description: The minimal size of bins in the main heatmap.

Accepted values: 0 .. 135
Value type: integer
Default value: 27
Button in GUI: View->Bins Minimum Bin Size (see in manual)

raw_size

Full parameter name: settings.interface.raw_size.val
Description: Size of the coverage plot.

Accepted values: 10 .. 500
Value type: integer
Default value: 50
Button in GUI: View->Panels Secondary data panel Size [pixel] (see in manual)

annotation

Full parameter name: settings.interface.show_hide.annotation
Description: Show or hide an element of the GUI / in the exported picture.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: View->Panels Show/Hide (see in manual)

axis

Full parameter name: settings.interface.show_hide.axis
Description: Show or hide an element of the GUI / in the exported picture.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: View->Panels Show/Hide (see in manual)

contig_borders

Full parameter name: settings.interface.show_hide.contig_borders
Description: Show or hide an element of the GUI / in the exported picture.

Accepted values: True, False
Value type: boolean
Default value: False
Button in GUI: View->Panels Show/Hide (see in manual)

coords

Full parameter name: settings.interface.show_hide.coords
Description: Show or hide an element of the GUI / in the exported picture.

Accepted values: True, False
Value type: boolean
Default value: False
Button in GUI: View->Panels Show/Hide (see in manual)

grid_lines

Full parameter name: settings.interface.show_hide.grid_lines
Description: Show or hide an element of the GUI / in the exported picture.

Accepted values: True, False
Value type: boolean
Default value: False
Button in GUI: View->Panels Show/Hide (see in manual)

heatmap

Full parameter name: settings.interface.show_hide.heatmap
Description: Show or hide an element of the GUI / in the exported picture.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: View->Panels Show/Hide (see in manual)

indent_line

Full parameter name: settings.interface.show_hide.indent_line
Description: Show or hide an element of the GUI / in the exported picture.

Accepted values: True, False
Value type: boolean
Default value: False
Button in GUI: View->Panels Show/Hide (see in manual)

raw

Full parameter name: settings.interface.show_hide.raw
Description: Show or hide an element of the GUI / in the exported picture.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: View->Panels Show/Hide (see in manual)

regs

Full parameter name: settings.interface.show_hide.regs
Description: Show or hide an element of the GUI / in the exported picture.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: View->Panels Show/Hide (see in manual)

tools

Full parameter name: settings.interface.show_hide.tools
Description: Show or hide an element of the GUI / in the exported picture.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: View->Panels Show/Hide (see in manual)

snap_bin_size

Full parameter name: settings.interface.snap_bin_size
Description: Restrict the allowed binsizes to round numbers. Does nothing for coordinates systems other than the genome.

Accepted values: True, False
Value type: boolean
Default value: False
Button in GUI: View->Bins Snap Bin Size (see in manual)

squared_bins

Full parameter name: settings.interface.squared_bins
Description: Enforce that bins are squares in the dataspace. Does nothing for coordinates systems other than the genome.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: View->Bins Make Bins Squares (see in manual)

tracks_log_scale

Full parameter name: settings.interface.tracks_log_scale
Description: For the secondary data panel: display the values on a log-scale

Accepted values: True, False
Value type: boolean
Default value: False
Button in GUI: View->Panels Display Tracks on a Log Scale (see in manual)

update_freq

Full parameter name: settings.interface.update_freq.val
Description: Delay between checking if the heatmap needs to be rerendered due to panning or zooming.

Accepted values: 0.1 .. 3
Value type: float
Default value: 0.5
Button in GUI: View->Rendering Update Frequency [seconds] (see in manual)

col

Full parameter name: settings.interface.v4c.col
Description: Set the Viewpoint (on the y-axis) for the Virtual 4C track of the columns.

Accepted values: text in the navigation syntax (see the ‘The Navigation bar’ chaper in the manual).
Value type: string
Button in GUI: View->Virtual4C Column Viewpoint (see in manual)

col_from

Full parameter name: settings.interface.v4c.col_from
Description: The start of the Viewpoint (on the y-axis) in index coordinates (i.e. at the base resolution of the index). Can be set more conveniently using settings.interface.v4c.col.

Accepted values: 0, 1, 2, 3, …
Value type: integer
Default value: 0
This parameter has no button in the GUI

col_to

Full parameter name: settings.interface.v4c.col_to
Description: The end of the Viewpoint (on the y-axis) in index coordinates (i.e. at the base resolution of the index). Can be set more conveniently using settings.interface.v4c.col.

Accepted values: 0, 1, 2, 3, …
Value type: integer
Default value: 10
This parameter has no button in the GUI

do_col

Full parameter name: settings.interface.v4c.do_col
Description: Compute a Virtual 4C track for the columns of the heatmap.

Accepted values: True, False
Value type: boolean
Default value: False
Button in GUI: View->Virtual4C Compute for columns (see in manual)

do_row

Full parameter name: settings.interface.v4c.do_row
Description: Compute a Virtual 4C track for the rows of the heatmap.

Accepted values: True, False
Value type: boolean
Default value: False
Button in GUI: View->Virtual4C Compute for rows (see in manual)

norm_by_viewpoint_size

Full parameter name: settings.interface.v4c.norm_by_viewpoint_size
Description: Normalize the virtual4C tracks by the size of the viewpoint.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: View->Virtual4C Normalize by viewpoint size (see in manual)

row

Full parameter name: settings.interface.v4c.row
Description: Set the Viewpoint (on the x-axis) for the Virtual 4C track of the rows.

Accepted values: text in the navigation syntax (see the ‘The Navigation bar’ chaper in the manual).
Value type: string
Button in GUI: View->Virtual4C Row Viewpoint (see in manual)

row_from

Full parameter name: settings.interface.v4c.row_from
Description: The start of the Viewpoint (on the x-axis) in index coordinates (i.e. at the base resolution of the index). Can be set more conveniently using settings.interface.v4c.col.

Accepted values: 0, 1, 2, 3, …
Value type: integer
Default value: 0
This parameter has no button in the GUI

row_to

Full parameter name: settings.interface.v4c.row_to
Description: The end of the Viewpoint (on the x-axis) in index coordinates (i.e. at the base resolution of the index). Can be set more conveniently using settings.interface.v4c.col.

Accepted values: 0, 1, 2, 3, …
Value type: integer
Default value: 10
This parameter has no button in the GUI

zero_track_at_ends

Full parameter name: settings.interface.zero_track_at_ends
Description: For the secondary data panel: draw an additional line-point at (0/0) and (0/end).

Accepted values: True, False
Value type: boolean
Default value: False
Button in GUI: View->Panels Zero Track at Ends (see in manual)

zoom_redraw

Full parameter name: settings.interface.zoom_redraw.val
Description: Redraw the heatmap if less than x% of the previously rendered heatmap area is visible.

Accepted values: 0 .. 100
Value type: integer
Default value: 90
Button in GUI: View->Rendering Redraw if zoomed in by [%] (see in manual)

The Normalization subgroup

color_range

Full parameter name: settings.normalization.color_range.val_min and settings.normalization.color_range.val_max
Description: range of the color scale of the main heatmap

Accepted values: 0 .. 1
Value type: float
Default value: 0.0 and 1.0
Button in GUI: View->Color Color Scale Range (see in manual)

ddd

Full parameter name: settings.normalization.ddd
Description: Normalize away the distance dependent decay.

Accepted values: True, False
Value type: boolean
Default value: False
Button in GUI: Normalize->DDD Normalize Primary data (see in manual)

ddd_all_samples

Full parameter name: settings.normalization.ddd_all_samples
Description: Compute distance dependent decay using all bins in the heatmap instead of sampling.

Accepted values: True, False
Value type: boolean
Default value: False
This parameter has no button in the GUI

ddd_quantile

Full parameter name: settings.normalization.ddd_quantile.val
Description: Exclude the top and bottom x% of samples when computing the distance dependant decay average.

Accepted values: 0 .. 100
Value type: integer
Default value: 80
Button in GUI: Normalize->DDD Percentile of samples to keep [%] (see in manual)

ddd_samples

Full parameter name: settings.normalization.ddd_samples.val_min and settings.normalization.ddd_samples.val_max
Description: Number of samples to compute for the distance dependant decay average. Will always try to compute as many samples as possible but never more than the maximum picked by this slider. Diagonals with less than the minimum amount will be masked out.

Accepted values: 1 .. 1000
Value type: integer
Default value: 1 and 200
Button in GUI: Normalize->DDD Number of samples (see in manual)

ddd_show

Full parameter name: settings.normalization.ddd_show
Description: Display distance dependent decay as a separate plot.

Accepted values: True, False
Value type: boolean
Default value: False
Button in GUI: Normalize->DDD Display (see in manual)

grid_seq_annotation

Full parameter name: settings.normalization.grid_seq_annotation
Description: Pick which annotation to compute the background for.

Accepted values: gene
Value type: string
Default value: gene
Button in GUI: Normalize->Primary->Assoc. Slices Annotation type (see in manual)

grid_seq_axis_is_column

Full parameter name: settings.normalization.grid_seq_axis_is_column
Description: If ticked, the normalization is applied column-wise, else row-wise.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: Normalize->Primary->Assoc. Slices Compute background for columns (see in manual)

grid_seq_display_background

Full parameter name: settings.normalization.grid_seq_display_background
Description: Display the sampled background in the secondary data panel.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: Normalize->Primary->Assoc. Slices Display Background as Secondary Data (see in manual)

grid_seq_dna_filter_v2

Full parameter name: settings.normalization.grid_seq_dna_filter_v2.val
Description: Acceptable minimal value for the maximal number of reads per kbp.

Accepted values: 0 .. 100000
Value type: integer
Default value: 0
Button in GUI: Normalize->Primary->Assoc. Slices Maximal DNA reads in bin minimum (see in manual)

grid_seq_filter_intersection

Full parameter name: settings.normalization.grid_seq_filter_intersection
Description: Use the minimum number of interactions between datasets (intersection) as background; otherwise use the maximum.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: Normalize->Primary->Assoc. Slices Use intersection between datasets (see in manual)

grid_seq_global

Full parameter name: settings.normalization.grid_seq_global
Description: Compute the assoc. slices normalization using all bins in the heatmap instead of sampling.

Accepted values: True, False
Value type: boolean
Default value: False
This parameter has no button in the GUI

grid_seq_ignore_cis

Full parameter name: settings.normalization.grid_seq_ignore_cis
Description: Ignore cis interactions during the computation of associated slices.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: Normalize->Primary->Assoc. Slices Ignore cis interactions (see in manual)

grid_seq_max_bin_size

Full parameter name: settings.normalization.grid_seq_max_bin_size.val
Description: Pick the binsize of the samples that are taken to determine Associated slices.

Accepted values: 1000 .. 100000
Value type: integer
Default value: 1000
Button in GUI: Normalize->Primary->Assoc. Slices Section size max coverage [bp] (see in manual)

grid_seq_rna_filter_v2

Full parameter name: settings.normalization.grid_seq_rna_filter_v2.val
Description: Acceptable minimal value for the average number of reads per kbp.

Accepted values: 0 .. 100000
Value type: integer
Default value: 0
Button in GUI: Normalize->Primary->Assoc. Slices RNA reads per kbp minimum (see in manual)

grid_seq_samples

Full parameter name: settings.normalization.grid_seq_samples.val
Description: When querying the coverage of replicates, query the maximal coverage per secion instead of the full coverage of the column.

Accepted values: 100 .. 10000
Value type: integer
Default value: 1000
Button in GUI: Normalize->Primary->Assoc. Slices Number of samples (see in manual)

ice_ignore_n_diags

Full parameter name: settings.normalization.ice_ignore_n_diags.val
Description: Ignore the n closest bins to the diagonal during ICing

Accepted values: 0 .. 10
Value type: integer
Default value: 2
Button in GUI: Normalize->Primary->Ic Ignore first n bins next to the diagonal (see in manual)

ice_local

Full parameter name: settings.normalization.ice_local
Description: Only use the visible bins to compute the IC bias.

Accepted values: True, False
Value type: boolean
Default value: False
Button in GUI: Normalize->Primary->Ic Local Ic (see in manual)

ice_mad_max

Full parameter name: settings.normalization.ice_mad_max.val
Description: Mad max filter

Accepted values: 0 .. 100
Value type: integer
Default value: 5
Button in GUI: Normalize->Primary->Ic Mad Max filter (see in manual)

ice_min_nz

Full parameter name: settings.normalization.ice_min_nz.val
Description: Minimal number of bins with non-zero values for a slice not to be blacked out during ICing

Accepted values: 0 .. 100
Value type: integer
Default value: 10
Button in GUI: Normalize->Primary->Ic Minimal number of non-zero bins per slice (see in manual)

ice_show_bias

Full parameter name: settings.normalization.ice_show_bias
Description: Display the IC bias as a track.

Accepted values: True, False
Value type: boolean
Default value: False
Button in GUI: Normalize->Primary->Ic Show Bias (see in manual)

ice_sparse_slice_filter

Full parameter name: settings.normalization.ice_sparse_slice_filter.val
Description: Filter out all slices where less than x percent of bins have a value larger than zero

Accepted values: 0 .. 100
Value type: integer
Default value: 10
Button in GUI: Normalize->Primary->Ic filter out slices with too many empty bins [%] (see in manual)

log_base

Full parameter name: settings.normalization.log_base.val
Description: logarithmic base for the color scale. Set to zero for a linear scale

Accepted values: 0 .. 15
Value type: float
Default value: 10.0
Button in GUI: View->Color Color Scale Log Base (see in manual)

min_interactions

Full parameter name: settings.normalization.min_interactions.val
Description: subtract this many interactions from each bin

Accepted values: 0 .. 100
Value type: integer
Default value: 0
Button in GUI: Filter->Datapools read-count adjustment (see in manual)

normalize_by

Full parameter name: settings.normalization.normalize_by
Description: normalize the matrix in various ways

Accepted values: rpm, rpk, radicl-seq, grid-seq, dont, ice
Value type: string
Default value: dont
Button in GUI: Normalize->Primary Normalize heatmap by (see in manual)

normalize_by_coverage

Full parameter name: settings.normalization.normalize_by_coverage
Description: normalize the coverage tracks in various ways

Accepted values: rpkb, rpmb, rpm, rpk, dont
Value type: string
Default value: rpkb
Button in GUI: Normalize->Primary Normalize coverage by (see in manual)

num_ice_bins

Full parameter name: settings.normalization.num_ice_bins.val
Description: The number of samples to compute during IC normalization.

Accepted values: 1 .. 1000
Value type: integer
Default value: 300
Button in GUI: Normalize->Primary->Ic Number of samples (see in manual)

p_accept

Full parameter name: settings.normalization.p_accept.val
Description: the acceptance p-value for the binominal test normalization. Does nothing for other normalizations.

Accepted values: 0.0 .. 0.1
Value type: float
Default value: 0.05
Button in GUI: Normalize->Primary->Binom. test pAccept for binomial test (see in manual)

ploidy_coords

Full parameter name: settings.normalization.ploidy_coords
Description: Use the contig order defined by the ploidy file. Otherwise the contig order defined by the sizes file is used.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: Normalize->Ploidy use ploidy corrected contigs (see in manual)

ploidy_correct

Full parameter name: settings.normalization.ploidy_correct
Description: Apply ploidy correction to the heatmap data.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: Normalize->Ploidy do correct (see in manual)

ploidy_keep_distinct_group

Full parameter name: settings.normalization.ploidy_keep_distinct_group
Description: During ploidy correction: Keep interactions from contig-pairs, where the two contigs never appear in the same ploidy group.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: Normalize->Ploidy Keep interactions from contig-pairs that never occur in the same group (see in manual)

ploidy_keep_inter_group

Full parameter name: settings.normalization.ploidy_keep_inter_group
Description: During ploidy correction: Keep interactions from instance-pairs, where the two instances are in the same group.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: Normalize->Ploidy Keep interactions from contig-pairs that are in the same group (see in manual)

ploidy_remove_intra_instance_contig

Full parameter name: settings.normalization.ploidy_remove_intra_instance_contig
Description: During ploidy correction: Remove interactions that are between two different instances of the same contig.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: Normalize->Ploidy Remove inter-contig, intra-instance interactions (see in manual)

ploidy_remove_others

Full parameter name: settings.normalization.ploidy_remove_others
Description: During ploidy correction: Remove interactions that are not explicitly kept/removed by any of the other options.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: Normalize->Ploidy Remove interactions that are not explicitly kept by the options above (see in manual)

radicl_local

Full parameter name: settings.normalization.radicl_local
Description: Compute the binominal test normalization using only bins from the currently visible area instead of sampling.

Accepted values: True, False
Value type: boolean
Default value: False
This parameter has no button in the GUI

radicl_seq_axis_is_column

Full parameter name: settings.normalization.radicl_seq_axis_is_column
Description: If ticked, the normalization is applied column-wise, else row-wise.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: Normalize->Primary->Binom. test Apply binomial test on columns (see in manual)

radicl_seq_display_coverage

Full parameter name: settings.normalization.radicl_seq_display_coverage
Description: Display the sampled coverage in the secondary data panel.

Accepted values: True, False
Value type: boolean
Default value: True
Button in GUI: Normalize->Primary->Binom. test Display Coverage as Secondary Data (see in manual)

radicl_seq_samples

Full parameter name: settings.normalization.radicl_seq_samples.val
Description: Number of samples used to determine the coverage of each slice. This coverage is then used in the binominal test.

Accepted values: 10 .. 1000
Value type: integer
Default value: 100
Button in GUI: Normalize->Primary->Binom. test Number of samples (see in manual)

scale

Full parameter name: settings.normalization.scale
Description: scale the final values of the main heatmap; where V is the set of all values, x’ a scaled and x the respective unscaled value.

Accepted values: abs, max, minmax, dont
Value type: string
Default value: max
Button in GUI: View->Color Color Range (see in manual)

The Replicates subgroup

between_group

Full parameter name: settings.replicates.between_group
Description: combine the two groups by…

Accepted values: sum, 1st, 2nd, sub, div, div+, dif
Value type: string
Default value: sum
Button in GUI: Filter->Datapools Compare datapools by (see in manual)

in_group

Full parameter name: settings.replicates.in_group
Description: combine the datasets that belong to the same group by…

Accepted values: sum, min, max, dif, mean
Value type: string
Default value: sum
Button in GUI: Filter->Datapools Merge datasets by (see in manual)