TY - GEN
T1 - In-Place Bijective Burrows-Wheeler Transforms
AU - Köppl, Dominik
AU - Hashimoto, Daiki
AU - Hendrian, Diptarama
AU - Shinohara, Ayumi
N1 - Funding Information:
Funding Dominik Köppl: JSPS KAKENHI Grant Number JP18F18120. Diptarama Hendrian: JSPS KAKENHI Grant Number JP19K20208. Ayumi Shinohara: JSPS KAKENHI Grant Number JP15H05706.
Publisher Copyright:
© 2020 Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. All rights reserved.
PY - 2020/6/1
Y1 - 2020/6/1
N2 - One of the most well-known variants of the Burrows-Wheeler transform (BWT) [Burrows and Wheeler, 1994] is the bijective BWT (BBWT) [Gil and Scott, arXiv 2012], which applies the extended BWT (EBWT) [Mantaci et al., TCS 2007] to the multiset of Lyndon factors of a given text. Since the EBWT is invertible, the BBWT is a bijective transform in the sense that the inverse image of the EBWT restores this multiset of Lyndon factors such that the original text can be obtained by sorting these factors in non-increasing order. In this paper, we present algorithms constructing or inverting the BBWT in-place using quadratic time. We also present conversions from the BBWT to the BWT, or vice versa, either (a) in-place using quadratic time, or (b) in the run-length compressed setting using O(n lg r/lg lg r) time with O(r lg n) bits of words, where r is the sum of character runs in the BWT and the BBWT. 2012 ACM Subject Classification Theory of computation; Mathematics of computing ! Combinatorics on words.
AB - One of the most well-known variants of the Burrows-Wheeler transform (BWT) [Burrows and Wheeler, 1994] is the bijective BWT (BBWT) [Gil and Scott, arXiv 2012], which applies the extended BWT (EBWT) [Mantaci et al., TCS 2007] to the multiset of Lyndon factors of a given text. Since the EBWT is invertible, the BBWT is a bijective transform in the sense that the inverse image of the EBWT restores this multiset of Lyndon factors such that the original text can be obtained by sorting these factors in non-increasing order. In this paper, we present algorithms constructing or inverting the BBWT in-place using quadratic time. We also present conversions from the BBWT to the BWT, or vice versa, either (a) in-place using quadratic time, or (b) in the run-length compressed setting using O(n lg r/lg lg r) time with O(r lg n) bits of words, where r is the sum of character runs in the BWT and the BBWT. 2012 ACM Subject Classification Theory of computation; Mathematics of computing ! Combinatorics on words.
KW - Burrows-wheeler transform
KW - In-place algorithms
KW - Lyndon words
UR - http://www.scopus.com/inward/record.url?scp=85088382615&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85088382615&partnerID=8YFLogxK
U2 - 10.4230/LIPIcs.CPM.2020.21
DO - 10.4230/LIPIcs.CPM.2020.21
M3 - Conference contribution
AN - SCOPUS:85088382615
T3 - Leibniz International Proceedings in Informatics, LIPIcs
BT - 31st Annual Symposium on Combinatorial Pattern Matching, CPM 2020
A2 - Gortz, Inge Li
A2 - Weimann, Oren
PB - Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
T2 - 31st Annual Symposium on Combinatorial Pattern Matching, CPM 2020
Y2 - 17 June 2020 through 19 June 2020
ER -