cifboot(1)
===========

NAME
----
cifboot - Produce bootstrap replicates of intensity data from an
Illumina sequencing machine.

SYNOPSIS
--------

*cifboot*   [-b boot] [-n nsample] [-p prefix] [-s seed] file

*cifboot*   --help

*cifboot*   --licence

DESCRIPTION
-----------
cifboot creates nonparametric bootstraps from a file containing
intensity data in CIF format from an Illumina sequencing machine. If
no file is specified, then cifboot reads from stdin.
Unless otherwise specified, the bootstrap sets of data contain the same
number of clusters as the original. Clusters are sampled uniformly
with replace, so the same cluster can be chosen many times (the
number of times each cluster is chosen being approximately Poisson
distributed with mean one).

*-b, --boot* nboot [default: 100]::
Number of bootstrap replicates to produce. Each replicate is written
to its own file.

*-n, --nsample* nsample [default: number of clusters]::
Number of clusters in each bootstrap. Default is the same as the
number as the input file.

*-p, --prefix* prefix [default: "boot_"]::
Prefix for bootstrap files. Output bootstrap files will be named
prefixXXX.cif, where XXX is XXX'th bootstrap field-width chosen to
accomodate maximum value.

*-s, --seed* seed [default: from clock]::
Seed for random number generator.

*-h, --help*::
Display information about usage and exit.

*--licence*::
Display licence terms and exit.

BUGS
----
Only an ordinary nonparametric bootstrap of the data is performed, so
individual clusters may appear several times in the output. This
behaviour is undesirable for some applications and there should
probably be a whitening option to add a small amount of noise to the
output, making each cluster unique.

AUTHOR
------
Written by Tim Massingham, tim.massingham@ebi.ac.uk

cifboot uses the optimised SFMT code for the Mersenne twister random
number generator produced by Mutsuo Saito and Makoto Matsumotom, which
is available from Hiroshima University under a three-clause BSD style
licence.

RESOURCES
---------
See <http://www.ebi.ac.uk/~timm/ciftools/>.

REFERENCES
----------
Erfron, B. (1994) An Introduction to the Bootstrap. Chapman and Hall.

COPYING
-------
Copyright (C) 2010 European Bioinformatics Institute. Free use of this 
software is granted under the terms of the GNU General Public License 
(GPL). See the file *COPYING* in the ciftools distribution or  
<http://www.gnu.org/licenses/gpl.html> for details.

The included SFMT library is copyright (C) 2006,2007 Mutsuo Saito,
Makoto Matsumoto and Hiroshima University, and is distributed under a
three-clause BSD style licence. Seee
<http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/>.

SEE ALSO
--------
ciftools(1), cifcat(1), cifinfo(1), cifjoin(1), cifsplit(1), int2cif(1)

