int2cif -r readlen file

int2cif --help

int2cif --licence


Converts the depreciate INT style format intensity files for the Illumina platform (e.g. s_2_0001_int.txt.gz) into CIF format files. If no file is given on the commandline, intensity information is read from stdin (and assumed to be uncompressed). The binary CIF output is written to stdout.

General INT data is stored to one decimal place whereas CIF intensity data is rounded to the nearest integer, so some precision is lost during the conversion. The CIF format does not contain the coordinates of the clusters.

-r, --readlen read length [required argument]

Number of cycles in intensity data to read.

-h, --help

Display information about usage and exit.


Display licence terms and exit.


Written by Tim Massingham,



Copyright © 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 for details.


ciftools(1), cifboot(1), cifcat(1), cifinfo(1), cifjoin(1), cifsplit(1)