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# call_alleles_test.py

## High-level description

This file contains unit tests for the allele calling functionality in the Cassiopeia library, specifically testing the `alignment_utilities.py` and `pipeline.py` modules. The tests cover various scenarios of CIGAR string parsing, indel detection, and allele calling for both basic and complex cases.

## Code Structure

The code is structured as a single test class `TestCallAlleles` that inherits from `unittest.TestCase`. It contains multiple test methods, each focusing on different aspects of allele calling and CIGAR string parsing. The `setUp` method initializes test data used across multiple test cases.

## Symbols

### TestCallAlleles

#### Description

A test class that contains multiple unit tests for the allele calling functionality in Cassiopeia.

#### Internal Logic

1. Sets up test data in the `setUp` method.
2. Implements various test methods to cover different scenarios of CIGAR string parsing and allele calling.
3. Uses assertions to verify the correctness of the results.

### setUp

#### Description

Initializes test data used across multiple test cases.

#### Internal Logic

1. Sets up basic and long reference sequences.
2. Defines barcode intervals and cutsite locations.
3. Creates test alignment dataframes.

### test\_basic\_cigar\_string\_match

#### Description

Tests parsing of a basic CIGAR string with only matches.

#### Internal Logic

1. Calls `alignment_utilities.parse_cigar` with a simple match case.
2. Asserts the correctness of the returned intBC and indels.

### test\_basic\_cigar\_string\_deletion

#### Description

Tests parsing of a CIGAR string with a deletion.

#### Internal Logic

1. Calls `alignment_utilities.parse_cigar` with a deletion case.
2. Asserts the correctness of the returned intBC and indels.

### test\_basic\_cigar\_string\_deletion\_with\_context

#### Description

Tests parsing of a CIGAR string with a deletion, including context information.

#### Internal Logic

1. Calls `alignment_utilities.parse_cigar` with a deletion case and context enabled.
2. Asserts the correctness of the returned intBC and indels, including context.

### test\_basic\_cigar\_string\_insertion

#### Description

Tests parsing of a CIGAR string with an insertion.

#### Internal Logic

1. Calls `alignment_utilities.parse_cigar` with an insertion case.
2. Asserts the correctness of the returned intBC and indels.

### test\_basic\_cigar\_string\_insertion\_with\_context

#### Description

Tests parsing of a CIGAR string with an insertion, including context information.

#### Internal Logic

1. Calls `alignment_utilities.parse_cigar` with an insertion case and context enabled.
2. Asserts the correctness of the returned intBC and indels, including context.

### test\_long\_cigar\_parsing\_no\_context

#### Description

Tests parsing of a long CIGAR string without context.

#### Internal Logic

1. Calls `alignment_utilities.parse_cigar` with a long CIGAR string.
2. Asserts the correctness of the returned intBC and indels for multiple cutsites.

### test\_long\_cigar\_parsing\_with\_context

#### Description

Tests parsing of a long CIGAR string with context.

#### Internal Logic

1. Calls `alignment_utilities.parse_cigar` with a long CIGAR string and context enabled.
2. Asserts the correctness of the returned intBC and indels for multiple cutsites, including context.

### test\_intersite\_deletion\_parsing

#### Description

Tests parsing of a CIGAR string with an intersite deletion.

#### Internal Logic

1. Calls `alignment_utilities.parse_cigar` with a CIGAR string containing an intersite deletion.
2. Asserts the correctness of the returned intBC and indels for multiple cutsites.

### test\_complex\_cigar\_parsing\_intersite\_deletion

#### Description

Tests parsing of a complex CIGAR string with multiple intersite deletions.

#### Internal Logic

1. Calls `alignment_utilities.parse_cigar` with a complex CIGAR string containing multiple intersite deletions.
2. Asserts the correctness of the returned intBC and indels for multiple cutsites.

### test\_call\_alleles\_function

#### Description

Tests the `call_alleles` function from the Cassiopeia preprocessing module.

#### Internal Logic

1. Calls `cassiopeia.pp.call_alleles` with test alignment data.
2. Verifies the structure of the returned molecule table.
3. Asserts the correctness of the called alleles and intBCs for each read.

### test\_missing\_data\_in\_allele\_throws\_warning

#### Description

Tests that a warning is raised when there is missing data in the allele calling process.

#### Internal Logic

1. Calls `cassiopeia.pp.call_alleles` with alignment data containing missing information.
2. Asserts that a `PreprocessWarning` is raised.

## Dependencies

| Dependency | Purpose                        |
| :--------- | :----------------------------- |
| unittest   | Provides the testing framework |
| numpy      | Used for numerical operations  |
| pandas     | Used for handling dataframes   |
| cassiopeia | The main library being tested  |

## Error Handling

The code uses assertions to verify the correctness of the results. It also tests for the raising of a `PreprocessWarning` in case of missing data.

This test suite provides comprehensive coverage for the allele calling functionality in Cassiopeia, ensuring that various scenarios of CIGAR string parsing and indel detection are handled correctly.