Adding a new output format

[karel-brinda]

Description

Adding support for an additional output format with bitmasks.

CLI

-f INT     output format [0]
           0: Kraken
           1: bit-mask format

Bit-mask format spec

Tab delimited text file with the following columns

1. read name
2. ref k-mer set name
3. read length
4. number of k-mer matches
5. coverage
6. k-mer hit bit-mask

Example

Read ACCCAC, k=3

read1	ref1	6	3	6	1011
read1	ref2	6	1	3	1000

[salikhov-kamil]

@karel-brinda what is "ref k-mer set name" here?

[salikhov-kamil]

and one more suggestion: let's remove old output format? (it is needed for tests only I guess)

[karel-brinda]

what is "ref k-mer set name" here?

name of the k-mer set (before @)

let's remove old output format

We need the old format, too. It's much more appropriate for long reads (image, e.g., 1 Mbp long read that has some matches with all reference k-mer sets; the bit-mask format may occupy even several GB per a single read).

[simonepignotti]

I suggest adding the read length as well (redundant, but useful).