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debian/2.0+dfsg-2

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kmc
===
KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files.
The homepage of the KMC project is http://sun.aei.polsl.pl/kmc

Instalation
==========
Before compilation you need to install some libraries and modify makefile.

The necessary libraries that should be installed on a computer are:
* Boost version 1.51 or higher (for Boost/filesystem and Boost/thread libraries)
   change BOOST_LIB and BOOST_H in makefile to the directories where Boost is installed.

The following libraries come with KMC in a binary (64-bit compiled for x86 platform) form.
If your system needs other binary formats, you should put the following libraries in src/kmc/libs:
* asmlib - for fast memcpy operation (http://www.agner.org/optimize/asmlib-instructions.pdf)
* libbzip2 - for support for bzip2-compressed input FASTQ/FASTA files (http://www.bzip.org/)
* zlib - for support for gzip-compressed input FASTQ/FASTA files (http://www.zlib.net/)

If needed, you can also redefine maximal length of k-mer, which is 256 in the current version.
Note: KMC is highly optimized and spends only as many bytes for k-mer (rounded up to 8) as
necessary, so using large values of MAX_K does not affect the KMC performance for short k-mers.

Some parts of KMC use C++11 features, so you need a compatible C++ compiler, e.g., gcc 4.7
or higher.

After that, you can run make to compile kmc and kmc_dump applications.


Directory structure
===================
.             - main directory of KMC (programs after compilation will be stored here)
kmer_counter  - source code of kmc program
kmer_counter/libs - compiled binary versions of libraries used by KMC
kmc_api       - C++ source codes implementing API; must be used by any program that
                wants to process databases produced by kmc
kmc_dump      - source codes of kmc_dump program listing k-mers in databases produced by kmc