cifsplit(1)
===========

NAME
----
cifsplit - Split a CIF into two by cycle.

SYNOPSIS
--------

*cifsplit*   [-o offset] [-s suffix] file

*cifsplit*   --help

*cifsplit*   --licence

DESCRIPTION
-----------
Split a CIF file containing intensity data from the Illumina
sequencing platform into two CIF files, the first containing cycles 
1 to offset (default offset being half the number of cycles) and the
second containing the remaining cycles. Examples where this is useful 
include the common case where a run was paired end and it is desirable 
to look at the ends separately, and more exotic cases like TRADIS data 
where the first few cycles are all from the same template and so not 
interesting.

If no file is given on the commandline, cifsplit reads from stdin.

*-o, --offset* offset [default: half number of cycles of file]::
Offset of second read in paired-end file. Run is split into two
at this offset, so pairs do not have to have equal length. The default is to
split the read equally in two.

*-s, --suffix* suffix [default: "_end"]::
Suffix which to add to names to identify pairs. The original file
"s_4_33.cif" will have pairs "s_4_33_end1.cif" and "s_4_33_end2.cif"
by default. If the read was read from stdin, pairs are written to
"intensities_end1.cif" and "intensities_end2.cif"

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

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

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

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

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.

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

