gsa-is

gSAIS and gSACA-K are algorithms to construct the suffix array (SA) for a string collection.

Note:

If you want a plug-and-play tool to compute SA, LCP, DA, GSA and BWT for string collections you can use this software: https://github.com/felipelouza/gsufsort

Introduction

gSAIS and gSACA-K [1, 2] extend the linear-time suffix sorting algorithms SAIS [3] and SACA-K [4] to compute SA for string collections, maintaining their theoretical bounds and improving their practical performance.

Moreover, gSAIS and gSACA-K can also compute the LCP-array (LCP) and the document array (DA) as a byproduct, with the same theoretical bounds.

Our algorithms, gSACA-K, gSACA-K+LCP and gSACA-K+DA are optimal for strings from constant alphabets.

Experimental results have shown that our algorithms are fast with a very small memory footprint.

Build requirements

An ANSI C Compiler (e.g. GNU GCC)

API

gsacak.h (the same for gsais.h)

/** @brief Computes the suffix array SA (LCP, DA) of T^cat in s[0..n-1]
 *
 *  @param s    input concatenated string, using separators s[i]=1 and with s[n-1]=0
 *  @param SA   Suffix array 
 *  @param LCP  LCP array 
 *  @param DA   Document array
 *  @param n    string length
 * 
 *  @return depth of the recursive calls.
 */
int gsacak(unsigned char *s, uint_t *SA, int_t *LCP, int_t *DA, uint_t n);

/** @brief Computes the suffix array SA (LCP, DA) of T^cat (integer) in s[0..n-1]
 *
 *  @param s    input concatenated string, using separators s[i]=1 and with s[n-1]=0
 *  @param SA   Suffix array 
 *  @param LCP  LCP array 
 *  @param DA   Document array
 *  @param n    string length
 *  @param k    alphabet size+2 (0 and 1 are reserved)
 * 
 *  @return depth of the recursive calls.
 */
int gsacak_int(int_text *s, uint_t *SA, int_t *LCP, int_t *DA, uint_t n, uint_t k);

Options

 int gsacak(s, SA, NULL, NULL, n) //computes only SA
 int gsacak(s, SA, LCP,  NULL, n) //computes SA and LCP
 int gsacak(s, SA, NULL, DA,   n) //computes SA and DA
 int gsacak(s, SA, LCP,  DA,   n) //computes SA, LCP and DA

Example

Compilation:

gcc -c gsacak.c experiments/external/malloc_count/malloc_count.c
gcc test.c -o test gsacak.o malloc_count.o -ldl

Run a test:

./test banana anaba anan

Output:

N = 18
Text = banana$anaba$anan$#
i	SA	DA	LCP	BWT	suffixes
0	18	3	0	$	#
1	6	0	0	a	$anaba$anan$#
2	12	1	0	a	$anan$#
3	17	2	0	n	$#
4	5	0	0	n	a$anaba$anan$#
5	11	1	1	b	a$anan$#
6	9	1	1	n	aba$anan$#
7	15	2	1	n	an$#
8	3	0	2	n	ana$anaba$anan$#
9	7	1	3	$	anaba$anan$#
10	13	2	3	$	anan$#
11	1	0	4	b	anana$anaba$anan$#
12	10	1	0	a	ba$anan$#
13	0	0	2	#	banana$anaba$anan$#
14	16	2	0	a	n$#
15	4	0	1	a	na$anaba$anan$#
16	8	1	2	a	naba$anan$#
17	14	2	2	a	nan$#
18	2	0	3	a	nana$anaba$anan$#
malloc_count ### exiting, total: 19,703, peak: 10,487, current: 0

Remark:

The peak memory 10,487 is exactly 10KB + 247 bytes. 10KB is the workspace and 247 (13*19 bytes) bytes is the space used by the concatenated string s and the arrays SA, LCP and DA (13*n bytes)

Strings larger than n=2^31 (2GB):

One can change to 64 bits integers adding -DM64=1 in the compilation or by changing M64 to 1 here: link.

Integer strings:

One can set the size (in bytes) of s[0..n-1] for integer alphabets: link

Document array:

One can set the size (in bytes) of DA[0..n-1]: link

Citation

Please, if you use this tool in an academic setting cite the following paper:

@article{LouzaGT17b,
 author    = {Felipe A. Louza and Simon Gog and Guilherme P. Telles},
 title     = {Inducing enhanced suffix arrays for string collections},
 journal   = {Theor. Comput. Sci.},
 volume    = {678},
 pages     = {22--39},
 year      = {2017},
 url       = {http://www.sciencedirect.com/science/article/pii/S0304397517302621},
 doi       = {10.1016/j.tcs.2017.03.039},
}

References

[1] Louza, F. A., Gog, S., Telles, G. P., Induced Suffix Sorting for String Collections. In Proc. DCC, pp. 43-58, 2016, IEEE.

[2] Louza, F. A., Gog, S., Telles, G. P., Inducing enhanced suffix arrays for string collections. Theor. Comput. Sci., vol. 678, pp. 22-39, 2017, Elsevier.

[3] Nong G., Zhang S., Chan W. H., Two efficient algorithms for linear time suffix array construction, IEEE Trans. Comput., vol. 60, no. 10, pp. 1471–1484, 2011

[4] Nong, G., Practical linear-time O(1)-workspace suffix sorting for constant alphabets, ACM Trans. Inform. Syst., vol. 31, no. 3, pp. 1–15, 2013

Thanks

Thanks to Giovanni Manzini, Giovanna Rosone and René de R. Sacramento by helpful suggestions and debugging.

felipelouza / gsa-is