├── .gitignore ├── LICENSE.txt ├── Makefile ├── NEWS.md ├── README.md ├── branch.c ├── cmd-log.sh ├── dict.c ├── format.c ├── graph.c ├── hit.c ├── ketopt.h ├── khashl.h ├── kseq.h ├── ksort.h ├── main.c ├── option.c ├── overlap.c ├── pangene.1 ├── pangene.h ├── pangene.js ├── pgpriv.h ├── read.c ├── sys.c ├── test ├── C4 │ ├── 21GRCh38-renamed.paf.gz │ ├── 22CHM13-renamed.paf.gz │ ├── 31_chimpanzee.paf.gz │ ├── 32_bonobo.paf.gz │ ├── 33_gorilla.paf.gz │ ├── 34_orangutan.paf.gz │ ├── 35_gibbon.paf.gz │ ├── 36_monkey.paf.gz │ ├── 37_marmoset.paf.gz │ ├── 90_HG00438.1.f1v2g.paf.gz │ ├── 90_HG00438.2.f1v2g.paf.gz │ ├── 90_HG00673.1.f1v2g.paf.gz │ ├── 90_HG00673.2.f1v2g.paf.gz │ ├── 90_HG00733.1.f1v2g.paf.gz │ ├── 90_HG00733.2.f1v2g.paf.gz │ ├── 90_HG01071.1.f1v2g.paf.gz │ ├── 90_HG01071.2.f1v2g.paf.gz │ ├── 90_HG01106.1.f1v2g.paf.gz │ ├── 90_HG01106.2.f1v2g.paf.gz │ ├── 90_HG01123.1.f1v2g.paf.gz │ ├── 90_HG01123.2.f1v2g.paf.gz │ ├── 90_HG01978.1.f1v2g.paf.gz │ ├── 90_HG01978.2.f1v2g.paf.gz │ ├── 90_HG02622.1.f1v2g.paf.gz │ ├── 90_HG02622.2.f1v2g.paf.gz │ ├── 90_HG02717.1.f1v2g.paf.gz │ ├── 90_HG02717.2.f1v2g.paf.gz │ ├── 90_HG03486.1.f1v2g.paf.gz │ ├── 90_HG03486.2.f1v2g.paf.gz │ ├── 90_HG03540.1.f1v2g.paf.gz │ ├── 90_HG03540.2.f1v2g.paf.gz │ ├── 90_NA19240.1.f1v2g.paf.gz │ └── 90_NA19240.2.f1v2g.paf.gz └── bubble │ ├── t1-1.gfa │ ├── t1-2.gfa │ ├── t1-3.gfa │ ├── t1-4.gfa │ ├── t1-5.gfa │ ├── t1-6.gfa │ ├── t1-7.gfa │ ├── t1-7a.gfa │ ├── t1-8.gfa │ ├── t1-8c.gfa │ ├── t2-0-simple.gfa │ ├── t2-1.gfa │ ├── t2-2.gfa │ ├── t2-3.gfa │ └── t2-4.gfa ├── tex ├── Makefile ├── README.md ├── pangene.bib └── pangene.tex └── vertex.c /.gitignore: -------------------------------------------------------------------------------- 1 | .*.swp 2 | *.o 3 | Makefile.bak 4 | -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- 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