faridrashidi/trisicell

Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data

trisicell's Issues

Cythonize issue for SCITE

Description

When Cythonizing the SCITE, there is an issue with the output.

Minimal reproducible example

Traceback

```pytb ```

Version

Sphinx docs failed in master branch

Description

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Minimal reproducible example

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Traceback

```pytb ... ```

Version

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change default of n_samples to an int in booster

Description

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Minimal reproducible example

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Traceback

```pytb ... ```

Version

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Consensus builder takes time on large instances

Description

Final step of consensus builder on large instances takes time.

Minimal reproducible example

trisicell consensus CRC01_T1_20k.CFMatrix CRC01_T2_10k.CFMatrix cons.CFMatrix

Traceback

```pytb ... ```

Version

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Consensus issue

Description

Error when trees have different cells

Minimal reproducible example

trisicell consensus example_input_1.CFMatrix example_input_2.CFMatrix output.CFMatrix

Traceback

```pytb Traceback (most recent call last):   File "run_trisicell.py", line 18, in     tsc.tl.consensus_tree(matrix_1, matrix_2)   File "/u/smalikic/anaconda3/lib/python3.8/site-packages/trisicell/tl/consensus/_consensus.py", line 209, in consensus_tree     common_cells = list(np.intersect1d(nodes1.keys(), nodes2.keys())[0]) IndexError: index 0 is out of bounds for axis 0 with size 0 ```

Version

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Joblib multithreaded error

Description

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Minimal reproducible example

trisicell search test.SC -p 4

Traceback

```pytb joblib.externals.loky.process_executor.TerminatedWorkerError: A worker process managed by the executor was unexpectedly terminated. This could be caused by a segmentation fault while calling the function or by an excessive memory usage causing the Operating System to kill the worker.

The exit codes of the workers are {EXIT(1)}

</details>

### Version
<!-- Output of trisicell.__version__ -->
v0.0.12