starchstrip1

Overview

starchstrip

USAGE: starchstrip [ --include | --exclude ] <chromosome-list> <starch-file>

* Add either the --include or --exclude argument to filter the specified

<starch-file> for chromosomes in <chromosome-list> for inclusion or exclusion, respectively. Note that you can only specify either inclusion or exclusion.

* The <chromosome-list> argument is a comma-separated list of chromosome names

to be included or excluded. This list is a *required* argument to either of the two --include and --exclude options.

* The output is a Starch archive containing those chromosomes specified for inclusion

or what chromosomes remain after exclusion from the original <starch-file>. A new metadata payload is appended to the output Starch archive.

* The output is written to the standard output stream -- use the output redirection

operator to write the result to a regular file, e.g.:

$ starchstrip --exclude chrA,chrB,chrC in.starch > out.starch

* If a specified chromosome is not in the input Starch archive, it will be ignored

during processing.

* Filtering simply copies over raw bytes from the input Starch archive and

no extraction or recompression is performed. Use 'starchcat' to update the metadata, if new attributes are required.

Process Flags -------------------------------------------------------------------------- --include <chromosome-list> Include specified chromosomes from <starch-file>.

--exclude <chromosome-list>

Exclude specified chromosomes from <starch-file>.

--version

Show binary version.

--help

Show this usage message.