├── .gitignore ├── LICENSE ├── Makefile_linux ├── Makefile_mac ├── README.md ├── configure ├── hera-EM ├── Hera-EM ├── LICENSE ├── Readme.md ├── align.c ├── align.h ├── bow_parser.c ├── bow_parser.h ├── build.sh ├── em.c ├── em.h ├── lendis.c ├── lendis.h ├── main.c ├── model.c ├── model.h ├── oridis.c ├── oridis.h ├── profile.c ├── profile.h ├── result.c ├── result.h ├── rspd.c ├── rspd.h ├── smodel.c ├── smodel.h ├── timing.h ├── transcript.c ├── transcript.h ├── transdis.c ├── transdis.h ├── utility.c ├── utility.h ├── utils.c └── utils.h └── src ├── EM.c ├── EM.h ├── argument.c ├── argument.h ├── assembly.c ├── bam_write.c ├── bam_write.h ├── bgzf.c ├── bgzf.h ├── fmindex.c ├── fmindex.h ├── fusion.c ├── fusion.h ├── genome_map.c ├── genome_map.h ├── get_buffer.c ├── get_buffer.h ├── hash_align.c ├── hash_align.h ├── hera_build ├── khash.h ├── kseq.h ├── log.c ├── log.h ├── macros.h ├── main.c ├── read.c ├── read.h ├── ssw.c ├── ssw.h ├── usage.c ├── usage.h ├── xxhash.c └── 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