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felipelouza / egsa

Generalized enhanced suffix array construction in external memory [CPM'13, AMB 2017]
https://doi.org/10.1186/s13015-017-0117-9
GNU General Public License v3.0
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How to read the output binary file? #1

Closed chjiao closed 6 years ago

chjiao commented 6 years ago

Hi, what is the format of the output binary file, how to read them in C++/C? Also, I am curious how you deal with the read index for generalized suffix array. When there are many reads, the read index may cost a lot of memory.

felipelouza commented 6 years ago

Hi, the output file .gesa can be read using esa_read_gsa(). Here is an example of such usage (check_gsa()). Alternatively, you can write your own procedure to read this struct t_GSA from the file. The read index is computed during the internal memory phase (esa_write_all()). We also consider this memory cost when we partition the input.