This homework is written in C++.
The resources I consulted when working on this assignment include:
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Provided C++ starter code
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Lecture slides on suffix arrays (for naive algorithms)
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Ben Langmead's original slides on suffix arrays (for simpaccel algorithms)
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Cereal library documentation (for serialization)
To build a suffix array with a given sequence in FASTA format , run the command below:
./buildsa reference output
Alternatively, to build a suffix array with a given sequence in FASTA format and generate a prefix table of length k, run the command below:
./buildsa --preftab k reference output_buildsa
To perform queries against the generated suffix array, run the command below (Query mode can be either naive or simpaccel):
./querysa index queries query_mode output_querysa