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Buffer size
Giovanna Rosone edited this page Mar 3, 2025
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One should set the following size of the buffers.
Please check BUFFERSIZE in TransposeFasta.h. It should be set based on the total available memory.
It means that BCR needs (max length of the reads) * BUFFERSIZE bytes in order to build the cyc files.
Please check SIZEBUFFER in parameters.h. It should be set based on the total available memory:
It means that BCR could need to (sizeof(bwt[i]) + sizeof(lcp[i]) + sizeof(da[i]) + sizeof(sa[i])) * SIZEBUFFER bytes in order to keep the I/O buffers.
You also keep in mind that it could use (sizeof(bwt[i]) + 2*sizeof(lcp[i]) + sizeof(da[i]) + sizeof(x)) bytes per text, where x is the type necessary to index the characters of the (complete) ebwt.