Commits · aa282e1cd9f22b3362dfb775c08e5223d22da94b · Lannoy, Carlos de / baseLess · GitLab

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Nov 05, 2021
- Merge branch 'master' into 'ben_dev' · aa282e1c
  Lannoy, Carlos de authored 3 years ago
  
  # Conflicts: # CnnParameterFile.yaml
  aa282e1c
- adapt threshold to logits · 3bc98026
  Carlos de Lannoy authored 3 years ago
  
  3bc98026
- add inference model class, more diverse neg examples, misc · 806d8816
  Carlos de Lannoy authored 3 years ago
  
  806d8816
- strided reads · d5aa0682
  Carlos de Lannoy authored 3 years ago
  
  d5aa0682
- remove old clutter · 78e5bc80
  Carlos de Lannoy authored 3 years ago
  
  78e5bc80
Nov 04, 2021
- Confusion matrix is now inferred from benchmark output, too · 244ca3ba
  Noordijk, Ben authored 3 years ago
  
  244ca3ba
- Merge remote-tracking branch 'origin/master' into ben_dev · 58f2f684
  Noordijk, Ben authored 3 years ago
  
  # Conflicts: # nns/Cnn_test.py
  58f2f684
- Proper squigglenet parser added now · e28c0d1c
  Noordijk, Ben authored 3 years ago
  
  e28c0d1c
Nov 03, 2021
- Squigglenet parsing stub · f55af93f
  Noordijk, Ben authored 3 years ago
  
  f55af93f
- fix accidental float-to-int casting, fix predict function · 9f2fe975
  Carlos de Lannoy authored 3 years ago
  
  9f2fe975
- Added script to visualise k-mer libraries · 8ece41cb
  Noordijk, Ben authored 3 years ago
  
  8ece41cb
- visualise_ground_truth_file.py can now be run from command line · 030cbcd5
  Noordijk, Ben authored 3 years ago
  
  030cbcd5
- Added support for multiprocessing, assert that input files are present and... · 5b0791b3
  Noordijk, Ben authored 3 years ago
  
  Added support for multiprocessing, assert that input files are present and fixed bug in F1 calculation for some species
  5b0791b3
- visualise_ground_truth_file.py now also shows species abundance · b9049d1d
  Noordijk, Ben authored 3 years ago
  
  b9049d1d
Nov 02, 2021
- Opens path object properly now · 86393885
  Noordijk, Ben authored 3 years ago
  
  86393885
- Run time analysis now parses all steps of the tools and saves figure to a file · c11af51a
  Noordijk, Ben authored 3 years ago
  
  c11af51a
- Added basic script that plots runtime of benchmark · 5378f7bc
  Noordijk, Ben authored 3 years ago
  
  5378f7bc
Nov 01, 2021
- lock-safe sql read/writes · 533d0c9c
  Carlos de Lannoy authored 3 years ago
  
  533d0c9c
- Added script to assess quality of ground truth data · b0e5ed2f
  Noordijk, Ben authored 3 years ago
  
  b0e5ed2f
- Removed superfluous dataframe processing · 12a14a66
  Noordijk, Ben authored 3 years ago
  
  12a14a66
- Ground truth parser now includes query length · cadda6a4
  Noordijk, Ben authored 3 years ago
  
  cadda6a4
- Ground truth parser now includes percent identity and alignment length · 535c250f
  Noordijk, Ben authored 3 years ago
  
  535c250f
Oct 29, 2021
- Now takes command line arguments · 8e404a0b
  Noordijk, Ben authored 3 years ago
  
  8e404a0b
- Hots hots, better plots · 9f44976b
  Noordijk, Ben authored 3 years ago
  
  9f44976b
- compare_accuracy.py now also parses guppy output and makes proper plots · 9cbec9d2
  Noordijk, Ben authored 3 years ago
  
  9cbec9d2
Oct 28, 2021
- Merge remote-tracking branch 'origin/master' into ben_dev · 8bae9293
  Noordijk, Ben authored 3 years ago
  
  8bae9293
- squigglenet_data_preparation.py can now be run from command line · c19ccdf6
  Noordijk, Ben authored 3 years ago
  
  c19ccdf6
- Added more documentation and basic plotting to accuracy evaluation · b1ce900a
  Noordijk, Ben authored 3 years ago
  
  b1ce900a
- less error-prone model loading · 9386da11
  Carlos de Lannoy authored 3 years ago
  
  9386da11
- Accuracy script now parses all uncalled and deepnano files in directories · a4c673ca
  Noordijk, Ben authored 3 years ago
  
  a4c673ca
- limit nb examples in dbs for validation · c3e2abd2
  Carlos de Lannoy authored 3 years ago
  
  c3e2abd2
Oct 27, 2021
- multiprocessing validation, misc · 3bd319d0
  Carlos de Lannoy authored 3 years ago
  
  3bd319d0
Oct 25, 2021
- Updated docstring · c1695251
  Noordijk, Ben authored 3 years ago
  
  c1695251
- Fixed duplicate species in ground_truth · dad676c4
  Noordijk, Ben authored 3 years ago
  
  dad676c4
Oct 24, 2021
- small fixes, update env · dbe6a5d7
  Lannoy, Carlos de authored 3 years ago
  
  dbe6a5d7
- add multi species 16S validation · 68456266
  Carlos de Lannoy authored 3 years ago
  
  68456266
Oct 22, 2021
- Expanded uncalled accuracy evaluation script · 728eaa55
  Noordijk, Ben authored 3 years ago
  
  728eaa55
- Removed some superfluous comments · 96817797
  Noordijk, Ben authored 3 years ago
  
  96817797
- Implemented first version of squiggle data preparation script · 327a1d89
  Noordijk, Ben authored 3 years ago
  
  327a1d89
- Hyperparameters as found by hyperopt · b8d346ff
  Noordijk, Ben authored 3 years ago
  
  b8d346ff