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Long input string is chopped in smaller units and builds suffix arrays in memory and dumps onto the disk.
For comparison, existing forward simulators are limited by the amount of sequence that can be stored in arrays in memory: for the aforementioned 20 000 individuals, 16 GB of memory would permit the storage of only 3.2 million base pairs of sequence per individual, which is an order of magnitude smaller than the smallest human chromosome.
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Precondition: The array pointer points to a valid non-NULL array in memory, and that array contains at least 'length' elements.
Precondition: The array pointer points to a valid non-NULL 2-D array in memory, and that array contains at least the given number of rows/columns.
Each pre-built per chromosome feature can be quickly loaded into a binned array in memory to support rapid lookup of any location in the chromosome and identify features within a given window size of the lookup location.
As stated in Section "Construction algorithm", when constructing the 1 Bloom structure, the only part written on the disk is T1 and it is read only once to fill an array in memory.
Apart from merely holding the arrays' data in memory, parallelization is needed to process those huge arrays within reasonable time.
The lack of spatial locality within the features in the SoA representation is illustrated in Figure 4; here, the SoA layout (on the left) stores pixels features in discontiguous 2D arrays (distant in memory) while for the AoS representation (on the right) features belonging to the same pixel are gathered together in contiguous memory addresses.
I therefore conclude that the PBWT-based approach can be hundreds of times faster than a direct search approach and find matches in time independent of the reference panel size, as conjectured above, so long as the associated index arrays fit in memory.
Since the RMON was configured with a 0.025-s time resolution and the PET scanner had a 0.001-s time resolution, we defined two arrays in computer memory representing 0.025-s 0.025-s of the trigger samples in the RMof (the trigger) and gate signals in the PET scanneRMONhe G array).
We defined each sample table as an array of unsigned chars and stored each array in flash memory, filling 12kB of memory on top of our program code.
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