alleles_to_bp_locs

This command can be used to find the contig and position corresponding to each of a set of alleles. The command takes in a table with a designated column containing allele IDs. It adds a column containing the location corresponding to the allele

Example:

alleles_to_bp_locs [arguments] < input > output

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 alleles_to_bp_locs. It is documented as follows:

Parameter and return types

$alleles is an alleles
$return is a reference to a hash where the key is an allele and the value is a bp_loc
alleles is a reference to a list where each element is an allele
allele is a string
bp_loc is a reference to a list containing 2 items:
	0: a contig
	1: an int
contig 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.