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genie.sh

README.md

GENIE

Setup

Add a [DATA].fa file to the data/ directory. For example, we have test.fa.

Running on Linux

Replace the gsed commands in ./genie.sh with sed. You may also have to add an #include <string.h> to build_bwt_index/file.cpp.

How to Run

  • Original implementations
    • Naive: ./genie.sh run_naive [DATA]. For example, with test.fa, run ./genie.sh run_naive test
    • Optimized: ./genie.sh run_opt [DATA]. For example, with test.fa, run ./genie.sh run_opt test
  • GENIE
    • Naive look up table (LUT): ./genie.sh run_lut [DATA]. For example, with test.fa, run ./genie.sh run_lut test
    • RMI: ./genie.sh run_rmi [DATA]. For example, with test.fa, run ./genie.sh run_rmi test

Clean

Run ./genie.sh clean [DATA]. For example, with test.fa, run ./genie.sh clean test.