vicleva/bloomfilter

C++ Bloom Filter implementation.

Has been made for an internship application.

Requirements:

• boost library
  (installation example : sudo apt install libboost-all-dev)
• c++ compiler
• FASTA file

ARGS:

• --help: produces help message
• --file: fasta file to map into the bloom filter
• --k: size of kmers <= 31
• --n: size of bloom filter in bits <= 2^34 (bits)
• --nf: number of applied hash functions <= 64
• --r: number of random is_present() tests

Use examples:

• Compilation:

g++ bf.cpp -lboost_program_options -o bf

• Execution:

  • ./bf --help
  • ./bf --file cov.fasta --k 10 --n 1048576 --nf 5 --r 100000
  • ./bf --file cov.fasta --k 31 --n 17179869184 --nf 64 --r 200 (max values for k, n, and nf)

Note:

It is possible to test a specific DNA Sequence in the main() by using the
compute_specific_requests(bf, string kmer); function.
There is already an example of size k=10 in bf.cpp at line 80.

(note 2 : ~ 9mins to build the filter with 752MB FASTA file)