.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH UNSTARCH "1" "October 2018" "unstarch 2.4.35+dfsg" "User Commands"
.SH NAME
unstarch \- manual page for unstarch 2.4.35+dfsg
.SH DESCRIPTION
unstarch
.IP
citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
.IP
https://doi.org/10.1093/bioinformatics/bts277
.IP
binary version: 2.4.35 (typical) (extracts archive version: 2.2.0 or older)
authors: Alex Reynolds and Shane Neph
.PP
USAGE: unstarch [ <chromosome> ]  [ \fB\-\-elements\fR |
.TP
\fB\-\-elements\-max\-string\-length\fR |
\fB\-\-bases\fR | \fB\-\-bases\-uniq\fR |
\fB\-\-has\-duplicates\fR | \fB\-\-has\-nested\fR | \fB\-\-list\fR |
\fB\-\-list\-json\fR | \fB\-\-list\-chromosomes\fR |
\fB\-\-archive\-timestamp\fR | \fB\-\-note\fR |
\fB\-\-archive\-version\fR | \fB\-\-is\-starch\fR |
\fB\-\-signature\fR | \fB\-\-verify\-signature\fR ]
<starch\-file>
.IP
Modifiers
\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
<chromosome>                     Optional. Either unarchives chromosomespecific records from the starch archive
.TP
file or restricts action of operator to
chromosome (e.g., chr1, chrY, etc.).
.IP
Process Flags
\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
\fB\-\-elements\fR                       Show total element count for archive. If
.TP
<chromosome> is specified, the result
shows the element count for the
chromosome.
.TP
\fB\-\-elements\-max\-string\-length\fR
Show the maximum string length over all
elements in <chromosome>, if specified.
If <chromosome> is not specified, the
maximum string length is shown over all
chromosomes.
.HP
\fB\-\-bases\fR,
.TP
\fB\-\-bases\-uniq\fR
Show total and unique base counts,
respectively, for archive. If
<chromosome> is specified, the count is
specific to the chromosome, if available.
.HP
\fB\-\-has\-duplicate\-as\-string\fR,
.TP
\fB\-\-has\-duplicate\fR
Show whether there is one or more
duplicate elements in the specified
chromosome, either as a numerical (1/0)
or string (true/false) value. If no
<chromosome> is specified, the value
given indicates if there is one or more
duplicate elements across all chromosome
records.
.HP
\fB\-\-has\-nested\-as\-string\fR,
.TP
\fB\-\-has\-nested\fR
Show whether there is one ore more nested
elements in the specified chromosome,
either as a numerical (1/0) or string
(true/false) value. If no <chromosome> is
specified, the value given indicates if
there is one or more nested elements
across all chromosome records.
.TP
\fB\-\-list\fR
List archive metadata (output is in text
format). If chromosome is specified, the
attributes of the given chromosome are
shown.
.HP
\fB\-\-list\-json\fR,
.TP
\fB\-\-list\-json\-no\-trailing\-newline\fR
List archive metadata (output is in JSON
format)
.HP
\fB\-\-list\-chr\fR,
.TP
\fB\-\-list\-chromosomes\fR
List all or specified chromosome in
starch archive (like "bedextract \fB\-\-listchr\fR"). If <chromosome> is specified but
is not in the output list, nothing is
returned.
.TP
\fB\-\-note\fR
Show descriptive note, if available.
.TP
\fB\-\-signature\fR
Display the Base64\-encoded SHA\-1 data
integrity signature for specified
<chromosome>, or the signatures of the
metadata and all available chromosomes,
if the <chromosome> is unspecified.
.TP
\fB\-\-verify\-signature\fR
Verify data integrity of specified
<chromosome>, or the integrity of all
available chromosomes, if the
<chromosome> is unspecified.
.TP
\fB\-\-archive\-timestamp\fR
Show archive creation timestamp (ISO 8601
format).
.TP
\fB\-\-archive\-type\fR
Show archive compression type.
.TP
\fB\-\-archive\-version\fR
Show archive version.
.TP
\fB\-\-is\-starch\fR
Test if <starch\-file> is a valid archive
and print 0/1 (false/true) to standard
output. Unstarch will also return a nonzero error code if the input file is not
a valid archive.
.TP
\fB\-\-version\fR
Show binary version.
.TP
\fB\-\-help\fR
Show this usage message.
.SH "SEE ALSO"
The full documentation for
.B unstarch
is maintained as a Texinfo manual.  If the
.B info
and
.B unstarch
programs are properly installed at your site, the command
.IP
.B info unstarch
.PP
should give you access to the complete manual.