Finding all maximal perfect haplotype blocks in linear time

Table 1 Running times and memory usage of our pBWT-based implementation

Data set	#lines	#columns	Min block size	Time	Memory (MB)	#blocks
chr. 22	5008	1,055,454		4 min 54 s	12.8	148,613,645
chr. 22	5008	1,055,454	500,000	3 min 50 s	12.8	16,076,453
chr. 22	5008	1,055,454	1,000,000	3 min 40 s	12.8	2,228,762
chr. 22	5008	1,055,454	2,000,000	3 min 43 s	12.8	4779
chr. 6	5008	4,800,101		19 min 42 s	12.8	624,689,548
chr. 6	5008	4,800,101	500,000	17 min 20 s	12.8	89,840,467
chr. 6	5008	4,800,101	1,000,000	16 min 30 s	12.8	11,388,982
chr. 6	5008	4,800,101	2,000,000	16 min 36 s	12.8	5585
chr. 2	5008	6,786,300		31 min 57 s	12.8	946,717,897
chr. 2	5008	6,786,300	500,000	25 min 06 s	12.8	160,094,115
chr. 2	5008	6,786,300	1,000,000	23 min 24 s	12.8	25,533,314
chr. 2	5008	6,786,300	2,000,000	23 min 18 s	12.8	120,243

Note that in our streaming implementation the memory usage is dominated by the number of haplotypes times the buffer size, and therefore is essentially constant in this study

ISSN: 1748-7188