KungFq Files

REQUIREMENTS

.NET 2.0 on Windows or mono (>=2.6) for Linux and Mac.

COMPILING AND RUNNING

If you want to compile the project you can either use Monodevelop
(opening the .sln) or Visual Studio (opening the .csproj) or run
./configure & make from a terminal.

Otherwise you can directly use the executables: on
Linux launch kungfq (bash script found in the KungFq_bin.tar.gz file) from
the decompressed directory KungFq_bin
and on Windows use KungFq_bin/KungFq.exe (file found in the KungFq_bin.zip file).

EXAMPLES and OPTIONS
Assuming that example.fastq is a fastq file with reads of 36 bases

to compress:
$ mono KungFq.exe -m encode -z gzip -l 36 example.fastq > example.kfq
or
$ mono KungFq.exe -m encode -z gzip -l 36 < example.fastq > example.kfq

to decompress:
$ mono KungFq.exe -m decode -z gzip -l 36 < example.qfq > example_decoded.fastq
or
$ mono KungFq.exe -m decode -z gzip -l 36 example.qfq > example_decoded.fastq

-z could be 'none', 'gzip' or 'lzma'. Lzma is slower but has a better
compression ratio, none should be used to further compress the
encoded data with other algorithms (note that one has to use the
same options when encoding/decoding the same file).
Warning: when encoding and using lzma the output can't be written on the
standard output therefore the desired file name should be the last argument
and for the same reason when decoding the compressed file name should be the
last argument and it should not be piped in the standard input.
For example:
$ mono KungFq.exe -m encode -z lzma -l 36 example.kfq < example.fastq
and
$ mono KungFq.exe -m decode -z lzma -l 36 example.kfq > example_decoded.fastq

-m and -l options are compulsory when one want to encode 
or decode a file; but if one only wants an histogram depicting
how many times the different quality values appear in the fastq it is
possible to just use -s with the desider prefix for the .txt and .svg
file that will be created. 
Therefore:
$ mono KungFq.exe -s example < example.fastq
will create two files: example.svg and example.txt (and will destroy
the previous contents of these files if they exist).

-i, used both when encoding and decoding, doesn't store the IDs and
creates numeric IDs for the decoded file (the read order
of the original file is preserved).

-q does the same with qualities (does not store them, but when
decoding the qualities lines of the fastq lacks completely).

-c sets the cutoff for quality values under
which corresponding base calls are converted to N. Use
the number corresponding to the desired ASCII character.

-s 'prefix'
can be used alone or when encoding a file and will create an
svg with the histogram of the quality values and a tab
delimited txt with observed quantities associated to quality values (see
the previous example).

-h will show an help message.