├── .gitignore ├── .gitlab-ci.yml ├── .gitmodules ├── .travis.yml ├── CMakeLists.txt ├── LICENSE.md ├── Makefile ├── ONT_logo.png ├── README.md ├── RELEASES.md ├── docker ├── Makefile ├── centos │ ├── centos_7_0_1406 │ │ └── Dockerfile │ ├── centos_7_1_1503 │ │ └── Dockerfile │ ├── centos_7_2_1511 │ │ └── Dockerfile │ ├── centos_7_3_1611 │ │ └── Dockerfile │ └── centos_7_4_1708 │ │ └── Dockerfile ├── debian │ ├── jessie │ │ └── Dockerfile │ └── stretch │ │ └── Dockerfile ├── opensuse │ ├── opensuse_42_2 │ │ └── Dockerfile │ └── opensuse_42_3 │ │ └── Dockerfile └── ubuntu │ ├── ubuntu_14_04 │ └── Dockerfile │ ├── ubuntu_16_04 │ └── Dockerfile │ ├── ubuntu_17_10 │ └── Dockerfile │ └── ubuntu_18_04 │ └── Dockerfile ├── interface └── scrappie.h ├── misc ├── alter_temperature.py ├── indent.sh ├── json_to_tsv.py ├── parse_events.py ├── parse_raw.py ├── parse_rgr.py ├── parse_rgrgr.py ├── parse_rgrgr_resgru.py ├── parse_rgrgr_reslstm.py ├── parse_rnnrf.py ├── parse_squiggle.py ├── skeleton_gru.py └── skeleton_lstm.py ├── python ├── LICENSE.md ├── MANIFEST.in ├── Makefile ├── OPENBLAS_LICENSE ├── README.md ├── build-wheels.sh ├── build.py ├── pyscrap.h ├── requirements.txt ├── scrappy │ └── __init__.py ├── setup.py └── test │ └── test_scrappy.py ├── reads ├── MINICOL228_20161012_FNFAB42578_MN17976_mux_scan_HG_52221_ch174_read172_strand.fa ├── MINICOL228_20161012_FNFAB42578_MN17976_mux_scan_HG_52221_ch174_read172_strand.fast5 ├── MINICOL228_20161012_FNFAB42578_MN17976_mux_scan_HG_52221_ch271_read66_strand.fa ├── MINICOL228_20161012_FNFAB42578_MN17976_mux_scan_HG_52221_ch271_read66_strand.fast5 ├── read_ch228_file118.fast5 └── test_squiggles.fa └── src ├── decode.c ├── decode.h ├── event_detection.c ├── event_detection.h ├── fast5_interface.c ├── fast5_interface.h ├── homopolymer.c ├── homopolymer.h ├── kseq.h ├── layers.c ├── layers.h ├── models ├── nanonet_events.h ├── raw_20170901_r94_4kHz_450bps_0b70da4.h ├── raw_r94.h ├── rgrgr-elu_20170914_r94_4kHz_450bps_ca2d1d1.h ├── rgrgr-elu_20180712_r941_4kHz_450bps_ed3b57a.h ├── rgrgr_r10.h ├── rgrgr_r10_tanh_20180719_90a6d26.h ├── rgrgr_r94.h ├── rgrgr_r941.h ├── rnnrf-elu_20171121_r94_4kHz_450bps_c2b6803.h ├── rnnrf_r94.h ├── squiggle_r10.h ├── squiggle_r10_20180518_244a3e3.h ├── squiggle_r94.h ├── squiggle_r94_20180502_9010ca3.h └── squiggle_r94_rna.h ├── networks.c ├── networks.h ├── nnfeatures.c ├── nnfeatures.h ├── scrappie.c ├── scrappie_common.c ├── scrappie_common.h ├── scrappie_event_table.c ├── scrappie_events.c ├── scrappie_help.c ├── scrappie_licence.h ├── scrappie_mappy.c ├── scrappie_matrix.c ├── scrappie_matrix.h ├── scrappie_raw.c ├── scrappie_seq_helpers.c ├── scrappie_seq_helpers.h ├── scrappie_seqmappy.c ├── scrappie_squiggle.c ├── scrappie_stdlib.h ├── scrappie_structures.h ├── scrappie_subcommands.c ├── scrappie_subcommands.h ├── sse_mathfun.h ├── test ├── Makefile ├── crp.py ├── normalised_signal.crp ├── path.crp ├── posterior_trimmed.crp 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