https://github.com/mbouzid/mphf
Indexing & querying matrix method with a minimal perfect hash function
https://github.com/mbouzid/mphf
big-data indexing-engine mphf
Last synced: 2 months ago
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Indexing & querying matrix method with a minimal perfect hash function
- Host: GitHub
- URL: https://github.com/mbouzid/mphf
- Owner: mbouzid
- Created: 2018-05-29T16:01:42.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2018-08-31T11:29:17.000Z (almost 7 years ago)
- Last Synced: 2024-10-06T04:03:12.188Z (8 months ago)
- Topics: big-data, indexing-engine, mphf
- Language: C++
- Homepage:
- Size: 319 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# mphf
## Dependencies
- sdsl-lite (git clone https://github.com/simongog/sdsl-lite.git)
## Acknowledgment
- BBHash (https://github.com/rizkg/BBHash)
## Install
` make && make clean `
## Usage
- indexing abundance k-mer matrix (w/compress)
` ./bin/mphf index [counts.tsv] [hash.bin] [counts.bin] y`
- file format for [counts.tsv]
```
tag sample1 ... sampleM
abundance11 ... abundance1M
...
abundanceN1 ... abundanceNM
```
e.g.
```
tag sample1 sample2 sample3 sample4
AAAAAAAAAAAAAAAAAAAAAAAAAAATTAT 12 78 11 91
CAAAAAAAAAAAAAAAAAAAAAAAAAAAATA 59 22 14 78
CCCTAAAAAAAAAAAAAAAAAAAAAAAAAAT 31 52 11 0
```
- querying k-mer
` ./bin/mphf query [counts.bin] [hash.bin] `
## Test
- index
`cd test && sh index.sh`
- query
`cd test && sh query.sh`