Common Reports Section

The configuration section for a common report follows the general INI format and must properly describe a common report for a single study. Its name must be commonReport - this will indicate that it is a common report section. This is an optional section.

Example Configuration

[commonReport]
enabled = yes

peopleGroups = status
groups = role:Role|status:Status|role,status:Role and Status

effect_groups = LGDs,nonsynonymous,UTRs
effect_types = Nonsense,Frame-shift,Splice-site,Missense,No-frame-shift
    noStart,noEnd,Synonymous,Non coding,Intron,Intergenic,3'-UTR,5'-UTR

draw_all_families = False
families_count_show_id = 3

[commonReport]

The properties for this section are explained below.

peopleGroups

peopleGroups = <comma-separated list of people groups>

peopleGroups is a comma-separated list of ids of people groups (defined in the People Group Section section in the study config), indicating for which people groups to generate the Families by pedigree part of common report.

groups

groups = <<column1>,<column2>:<name of common report group>|<column3>:<name of common report group>>

The format of this property is a list of common report groups separated by |. Each group is composed of two parts, separated by : - the first part is a comma-separated list of pedigree columns and the second is the name of the common report group.

This property defines the common report groups for the Families by number and De Novo Variants sections.

effect_groups

effect_groups = <comma-separated list of effect groups>

This property defines a list of effect groups for the De Novo Variants section of the common report. The effect groups are part of the variants query. Possible options for the effect groups and effect types that they contain are listed here.

effect_types

effect_types = <comma-separated list of effect types>

This property defines a list of effect types for the De Novo Variants section of the common report. The effect types are part of the variants query. Possible options for effect types are listed here.

draw_all_families

draw_all_families = <boolean>

This property defines whether to draw all families in the Families by pedigree section of the common report. This property takes a boolean value.

DEFAULT

families_count_show_id

families_count_show_id = <max amount of family pedigrees with a family ids list>

This property defines the maximum number of family pedigrees in the Families by number section of the common report for which to display a list of all family ids. Other family pedigrees will only have the amount of such families displayed. This property takes an integer value.

file_path

file_path = <string>

This property difines file path of the common report file.

DEFAULT

<directory of the config file>/common_report.json

enabled

enabled = <boolean>

DEFAULT

True

This property enables the common report functionality for the study. This property takes a boolean value.