mKD-GBWT

mKD-GBWT(multiple KD-tree GBWT) is an external memory full-text index.

The basis of mKD-GBWT is Geometric Burrows-Wheeler Transform. The biggest improvement of mKD-GBWT is that it uses multiple KD-tree as its orthogonal range searching data structure, so it has a good I/O performance.

Install

First you need install SAscan [1] and LCPscan [2].

[1] https://www.cs.helsinki.fi/group/pads/SAscan.html
[2] https://www.cs.helsinki.fi/group/pads/LCPscan.html
Download mKD-GBWT index from https://github.com/Hongweihuo-Lab/mKD-GBWT.

Modify the location of index

Open file sbt_util.h, modify the #define GBWT_INDEX_POSITION "/media/软件/GBWT-Index-position/" into location of yourself.
Open file tools/sam_sa_lcp.cpp, modify the #define GBWT_INDEX_POSITION "/media/软件/GBWT-Index-position/" into location of yourself.

$ cd mKD-GBWt $ make $ cd test $ make

Generate index of data

$ cd SAscan-??? $ cd src $ ./sascan
$ cd LCPscan-??? $ cd build $ ./construct_lcp
$ cd mKD-GBWT $ ./gen_sa_lcp
$ cd mKD-GBWT $ ./sam_sa_lcp $ ./build

Pattern-matching

$ cd mKD-GBWT     
$ ./mygbwt <data> <disk-page-size-in-bytes> <step>

Example

the data file is `/data/english`, disk-page is 4096 bytes, step = 4

First generate the index of data

	1. 	$ cd SAscan-???       
		$ cd src      
		$ ./sascan /data/english         

	2.	$ cd LCPscan-???    
		$ cd build     
		$ ./construct_lcp /data/english     

	3.	$ cd mKD-GBWT    
		$ ./gen_sa_lcp /data/english     

	4.	$ cd mKD-GBWT    
		$ ./sam_sa_lcp /data/english 4     
		$ ./build	/data/english	4096  	4     

Second, pattern mathcing

		$ cd mKD-GBWT    
		$ ./mygbwt /data/english 4096 4

Contributors

Code

• Yuhao Zhao （赵玉豪）

Paper

mKD-GBWT is an implementation of the paper.

Hongwei Huo, Yuhao Zhao, et al., Efficient external memory compressed indexes.

pucika / mKD-GBWT