region_to_alleles

Example:

region_to_alleles [-d 10000] < input > output

Here the region will be 20kb centered on the input positions.

The standard input should be a tab-separated table (i.e., each line is a tab-separated set of fields). Normally, the last field in each line would contain the identifer. If another column contains the identifier use

-c N

where N is the column (from 1) that contains the identifier.

This is a pipe command. The input is taken from the standard input, and the output is to the standard output.

Documentation for underlying call

This script is a wrapper for the CDMI-API call region_to_alleles. It is documented as follows:

Parameter and return types

$region_of_dna is a region_of_dna
$return is a reference to a list where each element is a reference to a list containing 2 items:
	0: an allele
	1: an int
region_of_dna is a reference to a list containing 4 items:
	0: a contig
	1: a begin
	2: a strand
	3: a length
contig is a string
begin is an int
strand is a string
length is an int
allele is a string

Command-Line Options

-c Column

This is used only if the column containing the identifier is not the last column.

-i InputFile [ use InputFile, rather than stdin ]

Output Format

The standard output is a tab-delimited file. It consists of the input file with extra columns added.

Input lines that cannot be extended are written to stderr.