homopolymer/SuffixArray

To build and manipulate suffix array

g++ -std=c++11 -o sa test.cpp SuffixArray.cpp

g++ -std=c++11 -o gsa test_gsa.cpp SuffixArray.cpp

time ./sa CGGTAATACGGAGGATCCAAGCGTTATCCGGAATCATTGGGTTTAAAGGGTCCGTAGGCGGTTTTATAAGTCAGTGGTGAAATCCGGCAGCTCAACTGTCGAACTGCCATTGATACTGTAGCGGTAATACGGAGGATCCAAGCGTTATCCGGAATCATTGGGTTTAAAGGGTCCGTAGGCGGTTTTATAAGTCAGTGGTGAAATCCGGCAGCTCAACTGTCGAACTGCCATTGATACTGTAGCGGTAATACGGAGGATCCAAGCGTTATCCGGAATCATTGGGTTTAAAGGGTCCGTAGGCGGTTTTATAAGTCAGTGGTGAAATCCGGCAGCTCAACTGTCGAACTGCCATTGATACTGTAGCGGTAATACGGAGGATCCAAGCGTTATCCGGAATCATTGGGTTTAAAGGGTCCGTAGGCGGTTTTATAAGTCAGTGGTGAAATCCGGCAGCTCAACTGTCGAACTGCCATTGATACTGTAGCGGTAATACGGAGGATCCAAGCGTTATCCGGAATCATTGGGTTTAAAGGGTCCGTAGGCGGTTTTATAAGTCAGTGGTGAAATCCGGCAGCTCAACTGTCGAACTGCCATTGATACTGTAG$