CMSC 701 Homework 1

Programming Language

This homework is written in C++.

References

The resources I consulted when working on this assignment include:

• Provided C++ starter code

• Lecture slides on suffix arrays (for naive algorithms)

• Ben Langmead's original slides on suffix arrays (for simpaccel algorithms)

• Standard C++ library reference

• Cereal library documentation (for serialization)

How to run

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