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
COLUMNREORDER	Reorder the columns by specifying source column and target column.	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
DEFLATECOLUMN	Compresses a column which meets minimum size requirement.	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
FILTERINVALIDROWS	Filters out invalid rows, e.g. rows missing columns.	GOR/NOR
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
GORIF	Checks existence of source files before running the GOR command.	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
GTTRANSPOSE	Generates one column named PNs and either one another column named VALUES, containing the genotypes of the pn by marker in the order defined by the marker source.	GOR
HIDE	Removes the listed columns from the output stream.	GOR/NOR
INFLATECOLUMN	De-compresses a column which has been compressed using DEFLATECOLUMN.	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
META	Allows querying of meta data associated with a data source.	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
NORIF	Checks existence of the source file before running the NOR command.	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
QUEEN	Calculates relationship statistics from a stream of horizontal genotypes.	GOR
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
SEGWHERE	Turns a stream of segments into a stream of non-overlapping segments based on a where condition.	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
SIGNATURE	Allows the control of create statements via time resolution or file changes.	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