Genotype-free demultiplexing of pooled single-cell RNA-Seq, using a hidden state model for identifying genetically distinct samples within a mixed population.
There are 2 pandas DataFrames being created in build_base_call_matrix(). However, their type is not explicitly set. Pandas sets it to np.int64 by default, which causes a huge amount of memory to be allocated. For big matrices it causes MemoryError:
I'm not sure, how big numbers in the matrices can be. But I believe, np.int16 would be more than enough. Please, set the type that matches the task.
There are 2 pandas DataFrames being created in![Screenshot from 2021-01-16 20-53-34](https://user-images.githubusercontent.com/35199218/104832503-1c814400-58c4-11eb-9075-fde5f6c30e05.png)
build_base_call_matrix()
. However, their type is not explicitly set. Pandas sets it tonp.int64
by default, which causes a huge amount of memory to be allocated. For big matrices it causes MemoryError:I'm not sure, how big numbers in the matrices can be. But I believe,
np.int16
would be more than enough. Please, set the type that matches the task.