Commands

A list of available GOR and NOR commands with descriptions

Command

Description

Context

ATMAX

Selects a single row based on a maximum value for a column.

GOR

ATMIN

Selects a single row based on a minimum value for a column.

GOR

BAMFLAG

Expands the FLAG bitmap column into multiple Boolean columns.

GOR

BASES

Separates the sequence read into the individual bases in the read based on the SEQ column.

GOR

BUCKETSPLIT

Split the content of a column into buckets based.

GOR/NOR

CALC

Add a calculated column to the output stream.

GOR/NOR

CALCIFMISSING

Add a calculated column to the output stream if it does not already exist.

GOR/NOR

CIGARSEGS

Separates the BAM-style sequence read into multiple reads based on the CIGAR column.

GOR

CMD

Run an external operating system command from within NOR.

GOR/NOR

COLNUM

Prefixes cell data with the number of the column in the output from which the cell data comes.

GOR/NOR

COLS2LIST

Collapse multiple columns to one list value.

GOR/NOR

COLSPLIT

Split the content of a column based on a defined split separator.

GOR/NOR

COLUMNSORT

Reorder the columns putting the specified columns at the beginning of the column list.

GOR/NOR

COLTYPE

Prefixes cell data with the type of the column in the output from which the cell data comes.

GOR/NOR

CSVCC

Aggregates or counts genotypes stored in horizontal CSV format.

GOR

CSVSEL

Selects a subset of data stored in a horizontal manner, as opposed to vertically in rows.

GOR

DAGMAP

Similar to MULTIMAP, but topologically ordering individuals based on their family tree relations.

GOR/NOR

DISTINCT

Eliminates duplicate rows from the output stream.

GOR/NOR

DISTLOC

Similar to TOP, but counting distinct loci instead of individual rows.

GOR

GAVA

Command for working with Gene Association

GOR

GOR

The core source command for working with genomic-ordered relational data.

GOR

GORCMD

Executes system commands that return tabular data within GOR queries.

GOR

GORROW

Returns a single row of data based on the input parameters.

GOR

GORROWS

Generates genomic ordered rows based on the input parameters.

GOR

GORSQL

Runs arbitrary commands against a database, which can be defined in a config file.

GOR

GRANNO

Aggregation and annotation in a single pass.

GOR/NOR

GREP

Filter for column content based on a specified expression.

GOR/NOR

GROUP

Aggregation of data based on a specified binsize and content of specified columns.

GOR/NOR

GTGEN

Generate genotypes in a horizontal bucket format.

GOR

GTLD

Calculate linkage disequilibrium between genotypes in different locations.

GOR

HIDE

Removes the listed columns from the output stream.

GOR/NOR

INSET

Only passes rows where the column value is found in the specified single-column setfile.

GOR/NOR

JOIN

Joins multiple sources (or a single source to itself) based on some defined overlap condition.

GOR

KING

Calculates relationship statistics from a stream of horizontal genotypes.

GOR

LEFTJOIN

A special type of join that returns all rows from the left source along with data from the right if any matches.

GOR

LEFTWHERE

Supplies additional join conditions into a left-join operation.

GOR

LIFTOVER

Converts GOR data from one reference genome build to another.

GOR

LOG

Specifies how often to log rows when monitoring the progress of a running query.

GOR/NOR

MAP

Joins together tables using columns other than the chromosome and position data.

GOR/NOR

MERGE

Combines two independent sources into a single genomic-ordered stream.

GOR/NOR

MULTIMAP

Similar to MAP, but with a mapfile that may contain a one-to-many mapping.

GOR/NOR

NOR

The core source command for working with non-ordered relational data.

NOR only

NORCMD

Executes system commands that return tabular data within NOR queries.

NOR only

NORROWS

Returns a specified number rows of data in a NOR context based on the input parameters.

NOR

NORSQL

Runs arbitrary commands against a database and the returned data can be used in a NOR context.

NOR

PARTGOR

Runs queries in parallel, partitioning the query execution along the tag-partition axis.

GOR

PEDPIVOT

Pivot a table using a pedigree file as a set of pivot points.

GOR/NOR

PGOR

Runs queries in parallel, partitioning the query execution along the genomic axis.

GOR

PILEUP

Describes the base-pair formation at each chromosomal position and summarises the base calls.

GOR

PIPESTEPS

Reads a number of analysis steps from a .yml file.

GOR

PIVOT

Extracts information from large row-based data sets and maps the data into horizontal columns.

GOR/NOR

PREFIX

Adds a specified prefix to the listed columns.

GOR/NOR

RANK

Adds a rank column based on a specified numeric column and binsize.

GOR/NOR

REGSEL

Grabs values from a source column based on a specified matching expression.

GOR/NOR

RELREMOVE

Removes related samples/individuals (PNs) from a phenotype relation.

NOR

RENAME

Renames a column in the output of a GOR or NOR query.

GOR/NOR

REPLACE

Similar to CALC, but replaces a specified column with the calculated values.

GOR/NOR

ROWNUM

Adds a column to the output stream with an auto-incrementing unique and sequential row number.

GOR/NOR

SDL

Runs arbitrary SDL commands against an SDL server and use the data in a NOR context.

NOR

SED

A search and replace function on the output stream. Maybe to applied to only specified rows.

GOR/NOR

SEGHIST

Turns a stream of annotations into a stream of non-overlapping segments.

GOR

SEGPROJ

Projects a stream of segments to provide a picture of the overlap between regions.

GOR

SEGSPAN

Turns a stream of segments into a stream of non-overlapping segments.

GOR

SELECT

Filters specified columns from the output stream.

GOR/NOR

SELWHERE

Filters specified columns from the output stream using an expression on column names/indices.

GOR/NOR

SEQ

Returns the corresponding reference sequence read for each row of the output (based on the position).

GOR

SETCOLTYPE

Sets column data types.

GOR/NOR

SKIP

Skips a specified number of rows before returning data.

GOR/NOR

SORT

Sorts the rows based on position in cases where the GOR condition has been violated.

GOR/NOR

SPLIT

Outputs multiple rows for columns that can be split based on a separator pattern.

GOR/NOR

TEE

Splits a GOR stream into two separate outputs based on a condition.

GOR/NOR

THROWIF

Throw an exception if the condition is satisfied.

GOR/NOR

TOP

Specify how many rows should be returned by the query.

GOR/NOR

TRYHIDE

Same as HIDE, but ignores errors generated from incorrect syntax.

GOR/NOR

TRYSELECT

Same as SELECT, but ignores errors generated from incorrect syntax.

GOR/NOR

TRYWHERE

Same as WHERE, but ignores errors generated from incorrect syntax.

GOR/NOR

UNPIVOT

Takes information in multiple rows and splits them into multiple rows as attribute-value pairs.

GOR/NOR

UNTIL

Terminates the stream when a condition is matched.

GOR/NOR

VARGROUP

Groups together variants with the same reference allele at a given position.

GOR

VARIANTS

Returns the variants found in sequence reads and their associated quality.

GOR

VARJOIN

Joins with an additional constraint that the columns denoting the reference and alternative alleles are equal.

GOR

VARMERGE

Ensures that overlapping variants are denoted in an equivalent manner.

GOR

VARNORM

Normalises the variation data in a gor stream to the left or the right.

GOR

VERIFYCOLTYPE

Ensures that the values in each row match their column type.

GOR/NOR

VERIFYORDER

Ensures that the genomic order of a GOR stream is correct, raising an exception if not.

GOR

VERIFYVARIANT

Ensures that the reference column corresponds to the configured build, raising an exception if not.

GOR

WAIT

Wait the specified number of milliseconds.

GOR/NOR

WHERE

Used to filter rows based on a specific conditional expression.

GOR/NOR

WRITE

Used to write a stream into one or more files simultaneously.

GOR/NOR