├── .gitignore ├── .gitmodules ├── CMakeLists.txt ├── LICENSE ├── README.md ├── data ├── BRCA1.vg └── reads.fa ├── ext ├── README.md ├── clipp.h └── kseq │ ├── LICENSE │ └── kseq.h ├── src ├── include │ ├── align.hpp │ ├── align_vectorized.hpp │ ├── base_types.hpp │ ├── csr.hpp │ ├── csr_char.hpp │ ├── graphLoad.hpp │ ├── graph_iter.hpp │ ├── parseCmdArgs.hpp │ └── utils.hpp └── main.cpp └── tests ├── CMakeLists.txt ├── data ├── BRCA1_16_uniform_len.fastq ├── BRCA1_1_read.fastq ├── BRCA1_5_reads.fastq ├── BRCA1_seq_graph.txt └── BRCA1_seq_graph.vg ├── test_graph_load.cpp ├── test_local_alignment.cpp ├── test_local_alignment_uniform_len.cpp └── test_pasgal_all.cpp /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ParBLiSS/PaSGAL/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: 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