├── .gitattributes ├── .gitignore ├── .gitlab-ci.yml ├── .travis.yml ├── CMakeLists.txt ├── LICENCE.txt ├── Makefile ├── ONT_logo.png ├── README.md ├── RELEASES.md ├── RUNNIE.md ├── images ├── ONT_logo.png ├── ONT_logo_590x106.png └── trace.png ├── misc ├── decode_runnie.py ├── parse_flipflop.py ├── parse_flipflop_guppy.py ├── parse_runlen.py ├── taiyaki_flipflop5_guppy.py ├── taiyaki_flipflop_guppy.py ├── taiyaki_rle.py ├── taiyaki_rle5.py ├── trace_flipflop.py └── trace_requirements.txt ├── reads ├── multi │ └── FAK40126_2fd3b110ca0d020049836a61f0dfb2b9983808f9_0.fast5 └── single │ ├── 0f776a08-1101-41d4-8097-89136494a46e.fast5 │ ├── 1f1a0f33-e2ac-431a-8f48-c3c687a7a7dc.fast5 │ ├── b7096acd-b528-474e-a863-51295d18d3de.fast5 │ ├── db6b45aa-5d21-45cf-a435-05fb8f12e839.fast5 │ └── de1508c4-755b-489e-9ffb-51af35c9a7e6.fast5 └── src ├── decode.c ├── decode.h ├── fast5_interface.c ├── fast5_interface.h ├── flappie.c ├── flappie_common.c ├── flappie_common.h ├── flappie_licence.h ├── flappie_matrix.c ├── flappie_matrix.h ├── flappie_output.c ├── flappie_output.h ├── flappie_stdlib.h ├── flappie_structures.c ├── flappie_structures.h ├── layers.c ├── layers.h ├── models ├── flipflop5_20200220_r103native_daa846e6.mdl ├── flipflop5_20200220_r941native_69216729.mdl ├── flipflop5_202003_r941native_5b1c1eee.mdl ├── flipflop5_202003_r941rna002_ff2161d3.mdl ├── flipflop5_r103native.h ├── flipflop5_r941native.h ├── flipflop5_r941rna002.h ├── flipflop_20181217_r941native5mC_4ad3b85.mdl ├── flipflop_r941native5mC.h ├── runlength5_202020_r941native_15b326ef.mdl └── runlength5_r941native.h ├── networks.c ├── networks.h ├── nnfeatures.c ├── nnfeatures.h ├── runnie.c ├── sse_mathfun.h ├── test ├── Makefile ├── crp.py ├── flappie_test_runner.c ├── flappie_util.c ├── flappie_util.h ├── gmon.out ├── normalised_signal.crp ├── path.crp ├── posterior_trimmed.crp ├── raw_signal.crp ├── read_crp.c ├── skeleton_rgr.c ├── test_common.h ├── test_flappie_convolution.c ├── test_flappie_elu.c 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