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# filter_bam_test.py

## High-level description

This file contains unit tests for the `filter_bam` function from the `cassiopeia.preprocess.pipeline` module. The tests verify that the function correctly filters BAM files based on a specified read quality threshold.

## Symbols

### `TestFilterBam`

#### Description

This is a test class that inherits from `unittest.TestCase`. It contains test methods to verify the functionality of the `filter_bam` function.

#### Internal Logic

1. Sets up the test environment by defining the path to a test BAM file.
2. Implements a test method `test_filter` to check the filtering functionality with different quality thresholds.

### `setUp`

#### Description

This method is called before each test method to set up the test environment.

#### Internal Logic

1. Determines the directory path of the current file.
2. Constructs the path to the test files directory.
3. Sets the path to a 10x Genomics v3 unmapped BAM file for testing.

### `test_filter`

#### Description

This method tests the `filter_bam` function with different quality thresholds.

#### Internal Logic

1. Calls `filter_bam` with a quality threshold of 10 and verifies that 2 alignments pass the filter.
2. Calls `filter_bam` with a quality threshold of 20 and verifies that 0 alignments pass the filter.
3. Uses `pysam.AlignmentFile` to read the filtered BAM files and count the number of alignments.
4. Uses `assertEqual` to check if the number of filtered alignments matches the expected count.

## Dependencies

| Dependency                     | Purpose                                                   |
| :----------------------------- | :-------------------------------------------------------- |
| os                             | File path operations                                      |
| unittest                       | Unit testing framework                                    |
| tempfile                       | Creating temporary directories                            |
| pysam                          | Reading BAM files                                         |
| ngs\_tools                     | Not directly used in the test file, but imported as `ngs` |
| cassiopeia.preprocess.pipeline | Module containing the `filter_bam` function being tested  |

## Error Handling

The test class uses the `unittest` framework's assertion methods to check for expected outcomes. If any assertion fails, the test will raise an exception, indicating a test failure.

## Notes

1. The test file uses a specific 10x Genomics v3 unmapped BAM file for testing, located in the "test\_files" directory.
2. The `filter_bam` function is called with temporary directories created using `tempfile.mkdtemp()` to store the output filtered BAM files.
3. The tests check two scenarios: one where some reads pass the quality filter (threshold 10) and another where no reads pass the filter (threshold 20).
4. The `pysam` library is used to read the filtered BAM files and count the number of alignments.
5. The `ngs_tools` module is imported but not used directly in this test file.