mbouzid/mphf

Indexing & querying matrix method with a minimal perfect hash function

C++

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
 <kmer1>  abundance11  ... abundance1M
   ...
 <kmerN> 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] <number of samples> <k-mer>

Test

index cd test && sh index.sh
query cd test && sh query.sh