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# convert_fastqs_to_unmapped_bam_test.py

Here's a detailed documentation of the target file `test/preprocess_tests/convert_fastqs_to_unmapped_bam_test.py`:

## High-level description

This file contains unit tests for the `convert_fastqs_to_unmapped_bam` function in the `cassiopeia.preprocess.pipeline` module. The tests verify the correct conversion of FASTQ files to unmapped BAM files for different sequencing chemistries.

## Code Structure

The main class `TestConvertFastqsToUnmappedBam` contains several test methods, each testing a different sequencing chemistry. The tests use sample FASTQ files and verify the correct conversion to BAM format, including proper tag assignments.

## Symbols

### TestConvertFastqsToUnmappedBam

#### Description

A unittest.TestCase subclass that contains test methods for the `convert_fastqs_to_unmapped_bam` function.

#### Internal Logic

* Sets up test FASTQ file paths in the `setUp` method
* Implements test methods for different sequencing chemistries (dropseq, 10xv2, 10xv3, indropsv3, slideseq2)
* Each test method:
  1. Calls `convert_fastqs_to_unmapped_bam` with appropriate parameters
  2. Reads the resulting BAM file
  3. Verifies the correct number of alignments, query names, sequences, and qualities
  4. Checks the correct assignment of BAM tags (UR, UY, CR, CY, RG)

### setUp

#### Description

Initializes the test environment by setting up file paths for test FASTQ files.

### test\_dropseq

#### Description

Tests the conversion of FASTQ files to BAM for the Drop-seq chemistry.

### test\_10xv2

#### Description

Tests the conversion of FASTQ files to BAM for the 10x Genomics v2 chemistry.

### test\_10xv3

#### Description

Tests the conversion of FASTQ files to BAM for the 10x Genomics v3 chemistry.

### test\_indropsv3

#### Description

Tests the conversion of FASTQ files to BAM for the inDrops v3 chemistry.

### test\_slideseq2

#### Description

Tests the conversion of FASTQ files to BAM for the Slide-seq v2 chemistry.

## Dependencies

| Dependency                     | Purpose                                     |
| :----------------------------- | :------------------------------------------ |
| os                             | File path operations                        |
| unittest                       | Unit testing framework                      |
| tempfile                       | Creating temporary directories              |
| pysam                          | Reading and manipulating BAM files          |
| ngs\_tools                     | FASTQ file handling                         |
| cassiopeia.preprocess.pipeline | Module containing the function being tested |

## Error Handling

The tests use assertions to verify the correctness of the BAM conversion. If any assertion fails, the test will raise an AssertionError, indicating a problem with the conversion process.

This test file is crucial for ensuring the correct functionality of the FASTQ to BAM conversion process in the Cassiopeia preprocessing pipeline, covering various sequencing chemistries and verifying the proper assignment of BAM tags.