contigs_to_md5s

contigs_to_md5s can be used to acquire MD5 values for each of a list of contigs. The quickest way to determine whether two contigs are identical is to compare their associated MD5 values, eliminating the need to retrieve the sequence of each and compare them.

The routine takes as input a list of contig IDs. The output is a mapping from contig ID to MD5 value.

Example:

contigs_to_md5s [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 subsystem.

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 contigs_to_md5s. It is documented as follows:

$return = $obj->contigs_to_md5s($contigs)

Parameter and return types

$contigs is a contigs
$return is a reference to a hash where the key is a contig and the value is a md5
contigs is a reference to a list where each element is a contig
contig is a string
md5 is a string

Command-Line Options

-c Column

This is used only if the column containing the subsystem 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 an extra column (the contig md5) added.

Input lines that cannot be extended are written to stderr.