colvalue

Format

cg colvalue ?options? ?infile? ?outfile?

Summary

Converts data in tsv format from a long key-value format to a wide column-value format

Description

In a file in long key-value format, each value is in a separate line, where each line has identifier fields indicating the object, key fields defining what the value descibes about the object, and a value field containing the actual value. "cg colvalue" converts these files to a wide col-value format, where all values about the object are on the same line in different columns.

The fields identifying the object can be specified using the -idfields option. If not given, all fields except the key and value fields will be used as idfields.

This command is similar to the cg wide command, but more generic. cg wide is specifically made for conveniently converting variant files (to wide variant file format with samples). cg colvalue can be used to "transpose" any tsv file.

Arguments

infile: file to be converted, if not given, uses stdin. File may be compressed.
outfile: write results to outfile, if not given, uses stdout

Options

-idfields list: which fields identify the object (default sample or id)
-keyfields keyfields: fields which compose the key. If more than one field is given, the fieldnames will be constructed by concatenating the values with - (default is key or parameter)
-valuefield: field containing the value (default value)

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