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

From: Finding all maximal perfect haplotype blocks in linear time

Data set#lines#columnsMin block sizeTimeMemory (MB)#blocks
chr. 2250081,055,454 4 min 54 s12.8148,613,645
chr. 2250081,055,454500,0003 min 50 s12.816,076,453
chr. 2250081,055,4541,000,0003 min 40 s12.82,228,762
chr. 2250081,055,4542,000,0003 min 43 s12.84779
chr. 650084,800,101 19 min 42 s12.8624,689,548
chr. 650084,800,101500,00017 min 20 s12.889,840,467
chr. 650084,800,1011,000,00016 min 30 s12.811,388,982
chr. 650084,800,1012,000,00016 min 36 s12.85585
chr. 250086,786,300 31 min 57 s12.8946,717,897
chr. 250086,786,300500,00025 min 06 s12.8160,094,115
chr. 250086,786,3001,000,00023 min 24 s12.825,533,314
chr. 250086,786,3002,000,00023 min 18 s12.8120,243
  1. 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