├── .gitignore ├── .gitmodules ├── .travis.yml ├── LICENSE ├── Makefile ├── README.md ├── edlib ├── include │ └── edlib.h └── src │ └── edlib.cpp ├── img ├── example_50x4.png ├── p.svg ├── phred.svg └── sigmoid.svg ├── ksw2 ├── ksw2.h ├── ksw2_extz2_sse.c └── ksw2_gg2_sse.c ├── simulation └── README.md ├── src ├── abpoa_cons.c ├── abpoa_cons.h ├── edlib_align.c ├── edlib_align.h ├── gen_cons.c ├── gen_cons.h ├── kdq.h ├── kseq.h ├── ksort.h ├── ksw2_align.c ├── ksw2_align.h ├── main.c ├── partition.c ├── partition.h ├── seq.c ├── seq.h ├── tab2fa.py ├── tandem_chain.c ├── tandem_chain.h ├── tandem_hit.c ├── tandem_hit.h ├── tidehunter.c ├── tidehunter.h ├── utils.c └── utils.h ├── test.fq └── test_data ├── 3prime.fa ├── 5prime.fa ├── full_length.fa ├── test_1000x10.fa └── test_50x4.fa /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Xinglab/TideHunter/HEAD/.gitignore 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