.TH "sindex" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"

.SH NAME
.TP 
sindex - index a sequence database for sfetch

.SH SYNOPSIS
.B sindex
.I [options]
.I seqfile1 [seqfile2...]

.SH DESCRIPTION

.B sindex
indexes one or more
.I seqfiles
for future sequence retrievals by 
.B sfetch.
An SSI ("squid sequence index") file is created in the same directory
with the sequence files. By default, this file is called 
.I <seqfile>.ssi.

.PP
If there is more than one sequence file on the command line,
the SSI filename will be constructed from the last sequence file
name. This may not be what you want; see the 
.I -o 
option to specify your own name for the SSI file.

.PP
.I sindex
is capable of indexing large files (>2 GB) if optional LFS support
has been enabled at compile-time. See INSTALL instructions that came
with @PACKAGE@.

.SH OPTIONS

.TP
.B -h
Print brief help; includes version number and summary of
all options, including expert options.

.TP
.BI -o " <ssi outfile>" 
Direct the SSI index to a file named
.I <outfile>.
By default, the SSI file would go to 
.I <seqfile>.ssi.

.SH EXPERT OPTIONS

.TP
.B --64
Force the SSI file into 64-bit (large seqfile) mode, even if the
seqfile is small. You don't want to do this unless you're debugging.

.TP
.B --external
Force 
.I sindex
to do its record sorting by external (on-disk) sorting. This is
only useful for debugging, too.

.TP
.BI --informat " <s>"
Specify that the sequence file is definitely in format 
.I <s>;
blocks sequence file format autodetection. This is useful in automated
pipelines, because it improves robustness (autodetection can
occasionally go wrong on a perversely malformed file). Common examples
include genbank, embl, gcg, pir, stockholm, clustal, msf, or phylip;
see the printed documentation for a complete list of accepted format
names.

.TP
.B --pfamseq
A hack for Pfam; indexes a FASTA file that is known to have identifier
lines in format ">[name] [accession] [optional description]". Normally
only the sequence name would be indexed as a primary key in a FASTA
SSI file, but this allows indexing both the name (as a primary key)
and accession (as a secondary key).

.SH SEE ALSO

.PP

.BR afetch (1),
.BR alistat (1),
.BR compalign (1),
.BR compstruct (1),
.BR revcomp (1),
.BR seqsplit (1),
.BR seqstat (1),
.BR sfetch (1),
.BR shuffle (1),
.BR sreformat (1),
.BR stranslate (1),
.BR weight (1).

.SH AUTHOR

Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
See COPYING in the source code distribution for more details, or contact me.

.nf
Sean Eddy
HHMI/Department of Genetics
Washington University School of Medicine
4444 Forest Park Blvd., Box 8510
St Louis, MO 63108 USA
Phone: 1-314-362-7666
FAX  : 1-314-362-2157
Email: eddy@genetics.wustl.edu
.fi