├── .gitignore ├── LICENSE ├── Makefile ├── README.md ├── dataset ├── dna-100.fasta ├── input-100.txt ├── input-10000.txt ├── long-reads-100.fastq ├── proteins-100.fasta ├── proteins-10000.fasta ├── reads-100.fastq └── reads-10000.fastq ├── external ├── SAscan-0.1.1 │ ├── AUTHORS │ ├── LICENCE │ ├── NEWS │ ├── README │ ├── VERSION │ └── src │ │ ├── Makefile │ │ ├── bitvector.h │ │ ├── external │ │ └── malloc_count │ │ │ ├── README.md │ │ │ ├── malloc_count.c │ │ │ ├── malloc_count.h │ │ │ ├── memprofile.h │ │ │ ├── stack_count.c │ │ │ ├── stack_count.h │ │ │ ├── test-malloc_count │ │ │ ├── Makefile │ │ │ └── test.c │ │ │ └── test-memprofile │ │ │ ├── Makefile │ │ │ ├── memprofile.gnuplot │ │ │ ├── memprofile.pdf │ │ │ └── test.cc │ │ ├── gap_array.h │ │ ├── main.cpp │ │ ├── merge.h │ │ ├── partial_sufsort.h │ │ ├── rank.h │ │ ├── sascan │ │ ├── sascan.h │ │ ├── settings.h │ │ ├── srank.h │ │ ├── stream.h │ │ ├── uint40.h │ │ ├── utils.cpp │ │ └── utils.h ├── gsaca-k.c ├── gsaca-k.h └── malloc_count │ ├── README.md │ ├── malloc_count.c │ ├── malloc_count.h │ ├── memprofile.h │ ├── stack_count.c │ ├── stack_count.h │ ├── test-malloc_count │ ├── Makefile │ └── test.c │ └── test-memprofile │ ├── Makefile │ ├── memprofile.gnuplot │ ├── memprofile.pdf │ └── test.cc ├── lib ├── defines.h ├── esa.c ├── esa.h ├── file.c ├── file.h ├── heap.c ├── heap.h ├── lcp.c ├── lcp.h ├── settings │ ├── defines.h │ ├── defines_1.h │ ├── defines_2.h │ ├── defines_3.h │ ├── defines_4.h │ ├── defines_5.h │ ├── defines_6.h │ ├── defines_7.h │ └── defines_8.h ├── utils.c └── utils.h ├── main.c ├── scripts ├── README ├── convert_fasta.c ├── tests-all.sh └── tests-esais.sh └── src ├── egsa.c └── egsa.h /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felipelouza/egsa/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: 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