What is it?
===========

Given a number of jellyfish databases, it outputs for all the k-mers
(in the union of the database) the number of occurrences in each of
the database.

LIMITATION: all the database must have been created with the same size
parameter to Jellyfish. It is adivsed to use the --disk switch of
'jellyfish count' to ensure that all the database are created with the
same size. For example: jellyfish count -s 100M --disk ...

The output is a column format where the first column is
the k-mer and the remaining columns are the counts in each of the
databases, in the same order as given on the command line.

For example:

$ ./count_in_file db1.jf db2.jf
GCCACGACTCGTGCA 1 0
CAAGCTGTGTGGCCG 0 2
CATAGAAATCGATAA 3 5
TACTATATAAGCAAA 2 0
...

Some details
============

The Jellyfish database are sorted list of k-mers. The sorting order is
based on the hash function (a random binary matrix). The program works
similarly to how merging sorted lists is done, but instead of summing
the count of each k-mers, it displays the count in each of the sorted
list.

Because all the files must be sorted according to the same criteria,
the size of the hash (and therefore the hash function) must be the
same for all the input files. See the LIMITATION paragraph above to
run Jellyfish properly. Note that the size passed to 'jellyfish count'
is NOT a limit on the number k-mers in the file (only a limit on the
number of mers in memory).
