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An implementation of a compressed suffix array based index with succinct longest common preffix information.
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README.md
alloc.c
alloc.h
bit.c
bit.h
compression.c
compression.h
config.cfg
control.c
csa.c
csa.h
dataStructures.c
dataStructures.h
debug.c
debug.h
definitions.h
global.c
global.h
main.c
makefile
search.c
search.h
suffixSort.c
suffixSort.h
textGenerator.c
utils.c
utils.h

README.md

Code disponibilized by: Daniel Saad and Mauricio Ayala-Rincón

danielsaad88@gmail.com ayala@unb.br

COMPILATION

In order to compile the source code, just do:

$ make

This will generate 3 executables:

  1. index - Our index.

  2. control - A program that uses libdivsufsort for comparison with our index.

  3. textGenerator - A program responsible to generate well formed files.

INPUT FILES

A well formed file, which is a text file that has the last symbol lexicographically smaller than the others. For example:

actagaccat$

EXECUTION

Here we show how to run the programs.

  1. index To create the index one must execute:

$ ./index -create

To search for ocurrences, one must do:

$ ./index -search

  1. control

    Same semantic from 1).

  2. textGenerator

    To generate a DNA well formed text, one must use:

$ textGenerator > dnaText.txt

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