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High-level description

This file defines the public API for the cassiopeia.preprocess module, exposing functions for preprocessing sequencing data into character matrices suitable for phylogenetic inference. It imports and re-exports specific functions from submodules, making them directly accessible through cassiopeia.preprocess.

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References

This file imports and re-exports symbols from the following files:
  • cassiopeia/preprocess/pipeline.py
  • cassiopeia/preprocess/utilities.py
  • cassiopeia/preprocess/setup_utilities.py

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Symbols

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Symbol Name

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__all__

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Description

A list of strings defining the public API of the cassiopeia.preprocess module. It specifies which symbols are exported when using from cassiopeia.preprocess import *.

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Inputs

N/A - This is a variable, not a function.

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Outputs

N/A - This is a variable, not a function.

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Internal Logic

The list includes functions for various preprocessing steps like sequence alignment, allele calling, UMI collapsing, data filtering, and lineage group calling. It also includes utility functions for data conversion and setup. 
__all__ = [
    "align_sequences",
    "call_alleles",
    "collapse_umis",
    "convert_fastqs_to_unmapped_bam",
    "error_correct_cellbcs_to_whitelist",
    "error_correct_intbcs_to_whitelist",
    "error_correct_umis",
    "filter_bam",
    "resolve_umi_sequence",
    "filter_molecule_table",
    "call_lineage_groups",
    "compute_empirical_indel_priors",
    "convert_alleletable_to_character_matrix",
    "convert_alleletable_to_lineage_profile",
    "convert_lineage_profile_to_character_matrix",
    "filter_cells",
    "filter_umis",
    "setup",
]