.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH STARCHSTRIP "1" "March 2024" "starchstrip 2.4.41+dfsg" "User Commands"
.SH NAME
starchstrip \- manual page for starchstrip 2.4.41+dfsg
.SH DESCRIPTION
starchstrip
.IP
citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
.IP
https://doi.org/10.1093/bioinformatics/bts277
.TP
version:
2.4.41 (typical)
.TP
authors:
Alex Reynolds and Shane Neph
.PP
USAGE: starchstrip [ \fB\-\-include\fR | \fB\-\-exclude\fR ] <chromosome\-list> <starch\-file>
.IP
* Add either the \fB\-\-include\fR or \fB\-\-exclude\fR argument to filter the specified
.IP
<starch\-file> for chromosomes in <chromosome\-list> for inclusion or
exclusion, respectively. Note that you can only specify either inclusion
or exclusion.
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* The <chromosome\-list> argument is a comma\-separated list of chromosome names
.IP
to be included or excluded. This list is a *required* argument to either of the
two \fB\-\-include\fR and \fB\-\-exclude\fR options.
.IP
* The output is a Starch archive containing those chromosomes specified for inclusion
.IP
or what chromosomes remain after exclusion from the original <starch\-file>. A new
metadata payload is appended to the output Starch archive.
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* The output is written to the standard output stream \fB\-\-\fR use the output redirection
.IP
operator to write the result to a regular file, e.g.:
.IP
\f(CW$ starchstrip --exclude chrA,chrB,chrC in.starch > out.starch\fR
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* If a specified chromosome is not in the input Starch archive, it will be ignored
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during processing.
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* Filtering simply copies over raw bytes from the input Starch archive and
.IP
no extraction or recompression is performed. Use 'starchcat' to update the
metadata, if new attributes are required.
.IP
Process Flags
\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
\fB\-\-include\fR <chromosome\-list>     Include specified chromosomes from <starch\-file>.
.TP
\fB\-\-exclude\fR <chromosome\-list>
Exclude specified chromosomes from <starch\-file>.
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\fB\-\-version\fR
Show binary version.
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\fB\-\-help\fR
Show this usage message.
.SH "SEE ALSO"
The full documentation for
.B starchstrip
is maintained as a Texinfo manual.  If the
.B info
and
.B starchstrip
programs are properly installed at your site, the command
.IP
.B info starchstrip
.PP
should give you access to the complete manual.