szhan/tsimpute

Issues

• Add argument to show chip sites or all sites to `create_sample_path_vis_app`

  #152 opened a year ago by szhan
  0

• Look into source code of BEAGLE 4.1

  #138 opened a year ago by szhan
  3

• Add mutations after adding new individuals to a tree sequence

  #144 opened a year ago by szhan
  1

• Add arguments to set bounds on site ids when visualising sample paths

  #149 opened a year ago by szhan
  0

• Add arguments to set bounds when visualising sample paths

  #147 opened a year ago by szhan
  1

• Refactor code to visualise sample paths

  #145 opened a year ago by szhan
  0

• Visualise LS HMM copying paths

  #64 opened a year ago by szhan
  14

• Parallelise `get_traceback_path`

  #106 opened a year ago by szhan
  5

• Append a bunch of sample edges at once to an existing tree sequence

  #140 opened a year ago by szhan
  0

• Refactor `make_compatible_genotypes`

  #136 opened a year ago by szhan
  0

• Package routines

  #70 opened a year ago by szhan
  1

• Add tests for `write_vcf` from tree sequences augmented by `add_individual_to_tree_sequence`

  #122 opened a year ago by szhan
  0

• Refactor `add_individual_to_tree_sequence`

  #123 opened a year ago by szhan
  1

• Visualise imputation performance

  #67 opened a year ago by szhan
  2

• Function to compare genotypes stored in `xarray.dataset` using `sgkit`

  #94 opened a year ago by szhan
  7

• Turn off `numba` when running tests on `get_matching_indices`

  #124 opened a year ago by szhan
  0

• Pass `Typed.List` to `get_matching_indices`

  #110 opened a year ago by szhan
  2

• Add `contig_length` when making compatible genotypes

  #131 opened a year ago by szhan
  0

• Keep VCF header when making compatible genotypes

  #113 opened a year ago by szhan
  1

• Freeze 'SamplePath' instances

  #129 opened a year ago by szhan
  1

• Make `is_valid` in `SamplePath` a class attribute

  #127 opened a year ago by szhan
  1

• Add tests for `add_individual_to_tree_sequence`

  #96 opened a year ago by szhan
  2

• Rework `impute_by_sample_matching` so that it doesn't take `SampleData` anymore

  #99 opened a year ago by szhan
  0

• Scale up `get_matching_indices`

  #102 opened a year ago by szhan
  2

• Allow for adding sample paths of an individual to an existing tree sequence

  #97 opened a year ago by szhan
  2

• Split `prepare_dataset.ipynb` into separate notebooks

  #93 opened a year ago by szhan
  1