felipelouza / remap

On the numbers of Lyndon factors from alphabet orderings

remap

This repository contains a set of methos for reordering the alphabet of a string T[1,n].

We investigate the effect of each alphabet reordering on the total number of Lyndon factors.

Build requirements

An C++ Compiler (e.g. GNU G++)

Example

Compilation:

make

Available options:

-A a	preferred algorithm to use (default 0)
-d D	use the first D documents of the INPUT
-b	read INPUT as binary input 
-f	read INPUT as (default) formatted input (.txt, .fasta or .fastq)
-v	verbose output
-s	compute the number of Lyndon Factors and the maximum length
-o  output converted file
-l  output the lyndon-factors (start positions) to (INPUT.pos)
-L  output the lyndon-factors (substrings) to (INPUT.lyn)
-p P	print the first P Lyndon factors (for debug)
-h	this help message

Notes:

• Supported extensions are .txt, .fasta and .fastq.

Algorithms:

-A	Algorithm	Output
0	None	Identity alphabet
1	LFS	Least Frenquent Symbol
2	MFS	Most Frenquent Symbol
7	Random	Randomize permutation

Run a test:

./remap -A 7 -v ../dataset/reads.fastq

Output:

Command line:
 ./remap -A 7 -v ../dataset/reads.fastq
d = 10000
N = 946583 bytes
sizeof(int) = 4 bytes
## RANDOM ##
A: G
C: N
G: A
N: C
T: T
##
Number of Lyndon factors: 15
Average length: 63105.53
Maximum length: 605983
##
15	63105.53	605983