bloom-filter

Bloom filter implementation for BIN-702

Getting Started

> clone the repository  
> run the main.py to start the benchmarks

Prerequisites

python 3.X
mmh3 lib -> pip install mmh3

Running the benchmark

> cd src/  
> python main.py

Benchmark results

Set	mb	peak mb	insert ms	clear ms	find ms
1000	0.000296	0.041276	0.9889	0	0
10000	0.000296	0.655676	1.9998	0	0
100000	0.000324	6.291772	19.9799	1.9973	8.9914
2000000	0.000324	100.663612	457.532	50.9484	203.3379

Bloom	mb	peak mb	insert ms	clear ms	find ms	error prob	hash count	bit count	error count
1000	0.010876	0.011449	15.9934	0	15.9833	0.001	7	9586	1
10000	0.0993	0.099879	179.8307	1.9978	155.8389	0.0021	7	95851	21
100000	1.04424	1.044825	1634.4944	44.9578	1571.1436	0.00154	7	958506	154
2000000	19.83744	19.838031	35077.5659	1017.1684	35077.5659	0.0016655	7	19170117	3331

Bloom	mb	peak mb	insert ms	clear ms	find ms	error prob	hash count	bit count	error count
1000	0.000296	0.041276	11.9879	0	12.9987	0.003	5	9586	3
10000	0.0993	0.099882	170.8237	1.9972	126.8831	0.0037	5	95851	37
100000	1.04424	1.044825	1246.7373	48.9547	1311.182	0.00221	5	958506	221
2000000	19.83744	19.838034	25255.1331	1037.1826	23715.8606	0.002236	5	19170117	4472

Bloom	mb	peak mb	insert ms	clear ms	find ms	error prob	hash count	bit count	error count
1000	0.00398	0.004556	12.9867	0.9983	15.9839	0.108	5	2949	108
10000	0.030796	0.031378	122.8838	0.9991	115.8721	0.1099	5	29492	1099
100000	0.321784	0.322372	1205.3608	11.9547	1442.8068	0.10759	5	294924	10759
2000000	6.10908	6.109674	24957.1912	330.6803	24417.6577	0.1064285	5	5898497	212857

Possible Applications in Bioinformatics

• Sequence characterization
• Genome assembly
• Sequencing error correction
• RNA-Seq

License

MIT

Authors

Tristan Deschamps