GitHub - giavjeko/bio: Computing the longest common prefix array based on the Burrows–Wheeler transform

Bioinformatics student project.

Installing

Clone this repo from github:

git clone --recursive https://github.com/giavjeko/bio.git

Once in the repo directory: (replace myusergroup with your user group)

sudo ./measure --setup -g myusergroup --perm 775
make

To run tests on all modules run make test

Run ./lcp [input_file_path] [output_file_path] Test input and correct output files are located in files directory

To run automated algorythm analysis run

./analysis.sh

Name		Name	Last commit message	Last commit date
Latest commit History 92 Commits
cgmemtime @ 6a7488d		cgmemtime @ 6a7488d
doc		doc
files		files
.gitignore		.gitignore
.gitmodules		.gitmodules
LICENCE		LICENCE
Makefile		Makefile
README.md		README.md
analysis.sh		analysis.sh
analysis_report.txt		analysis_report.txt
bitvector.c		bitvector.c
bitvector_test.c		bitvector_test.c
brute.py		brute.py
bwt.c		bwt.c
bwt_analysis.c		bwt_analysis.c
bwt_test.c		bwt_test.c
gen.c		gen.c
io.c		io.c
lcp.c		lcp.c
list.c		list.c
list_test.c		list_test.c
measure		measure
queue.c		queue.c
queue_test.c		queue_test.c
sais.c		sais.c
sais.h		sais.h
set.c		set.c
set_test.c		set_test.c
test.sh		test.sh
wtree.c		wtree.c
wtree_analysis.c		wtree_analysis.c
wtree_test.c		wtree_test.c