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CAF C TOOLS V2.0 21/06/2005
----------------------------------
This is V2.0 of the CAF (Common Assembly Format) C-tools. It comprises a set
of libraries and programs for manipulating DNA sequence assemblies using
CAF files.
The CAF specification can be found at:
http://www.sanger.ac.uk/Software/formats/CAF/
PROGRAMS
--------
Programs in this distribution include:
cafcat - Copies a caf file
caf_pad - Convert a CAF file from unpadded to padded format
caf_depad - Convert a CAF file from padded to unpadded format
caf2phrap - Dump fasta and quality files suitable for assembly with phrap
nd_clip - Vector or quality clip reads in a CAF assembly
caf2ace - Convert a CAF file to consed .ace format
cafmerge - Merge CAF files together (obsolete)
phrapcons - Tags contigs at points of low base confidence
caf_find_misassemblies
- Tags bases with high quality discrepancies and apparantly
misassembled reads
caf_check_pads
- Looks for places in an assembly where poor alignments may have
caused extra bases to appear in the consensus
templates - Print information about read locations in an assembly
caf2fastq - Dump reads in a CAF file in fastq format for use with the phusion
assembler
caf2gap - Convert a CAF format assembly to a gap4 database
These require the Staden io_lib. They are only really useful if you are not
using base confidence scores in your assemblies.
np_edit - Propose automatic read edits
nd_edit - Do automatic read edits
INSTALLATION
-------------
This new version of the package has been converted to use GNU automake and
autoconf. However, if you just want to build the package, then these tools
are not needed. Everything else you need should be included in this
package, apart from the Staden io_lib, which is optional.
It is possible to build the package either in the package source tree, or
in a 'build tree' (i.e. a directory that you create to put a specific build
of the package in). The latter is useful if you want to support multiple
architectures or want versions with and without debugging support.
For a build in the source tree, do:
./configure
make && make check && make install
(You may have to run make install as root, depending on where you want
to install the package).
NB: The makefiles that get built may not work with your native version of
make. If this is the case, try GNU make instead.
For a build tree, create the directory, cd into it and then run the
configure script in the source tree. E.g., if you are currently in the
source tree, you could do:
mkdir build
cd build
../configure
make && make check && make install
CONFIGURE OPTIONS
========= =======
The configure script takes all of the standard configure options. The
most useful is --prefix which can be used to change the location where
the binaries will be installed, e.g.
./configure --prefix=/usr/opt/caftools
Run:
./configure --help
for a list of options.
If you have a copy of the Staden io_lib (see http://staden.sourceforge.net/)
you can use the option --with-io_lib=/path/to/io_lib to build some optional
programs that require this library (including Richard Mott's auto-edit).
The majority of the programs will build without the need for io_lib, so
it is reasonable to ignore this for most builds.
It is also possible to set makefile variables on the configure script command
line, e.g.:
./configure CC=icc
will make all of the makefiles use icc for the C compiler (on intel, at least).
ARCHITECTURES
=============
The package has been built on the following architectures:
Platform OS Compiler
-------- -- --------
Alpha Tru-64 unix cc
Alpha Tru-64 unix gcc
i686 Linux gcc
i686 Linux icc
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