build

To use avx-512 instruction, for pop-count, compile with

cmake -DPOP_COUNT=AVX512

It might not be supported by your cpu.
lscpu should contain avx512_vpopcntdq, but this only mean it compiles correctly, it can still not work properly.

If avx-512 instructions are not supported, you can instead use avx instructions:

cmake -DPOP_COUNT=AVX

If avx is not supported at all, you can use

cmake -DPOP_COUNT=BASIC

The default is

cmake -DPOP_COUNT=DETECT

which tries to detect the best option for your system based on the available compile options. The fastest option is AVX512 followed by AVX.

run

./IBB-cli [-i <input_file>] [-o <output_file>] [-t <temp_dir>] [-k <layers>] [-p <processor_count>]

Layers affects the amount of RAM used. Higher Layers in the implementation use more RAM.

Defaults

• layers k: 5
• processors p: 1
• temp_dir t: directory where output_file o is.

In the temporary directory t, $2 * 2^{Layers-1}$ files will be generated.

Benötigte Strukturen

Datei

Dies muss von folgendem Format sein:

>SequenceX
ACGTACGATGTATGCTAGTCGTACGTAGTCTGATGCGTAGTCGTACGTAGTCGTAGTCCATTGCAGTCATGC
>SequenceX+1
ACTGCAGT

Allgemein:

((^>.*$) | (^[ACGT]+$))*

Kommentarzeilen beginnen mit einem > und enden mit dem Zeilenumbruch
Datenzeilen enthalten nur A, C, G oder T und enden mit einem Zeilenumbruch