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223 changes: 223 additions & 0 deletions .codeboarding/BeadArrayUtility.md
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```mermaid

graph LR

BeadArrayUtility["BeadArrayUtility"]

BeadPoolManifestParser["BeadPoolManifestParser"]

ClusterFileParser["ClusterFileParser"]

GenotypeCallsManager["GenotypeCallsManager"]

ScannerDataReader["ScannerDataReader"]

BeadPoolManifestParser -- "uses" --> BeadArrayUtility

ClusterFileParser -- "uses" --> BeadArrayUtility

GenotypeCallsManager -- "uses" --> BeadArrayUtility

GenotypeCallsManager -- "uses" --> BeadPoolManifestParser

ScannerDataReader -- "uses" --> BeadArrayUtility

GenotypeCallsManager -- "integrates" --> ScannerDataReader

```

[![CodeBoarding](https://img.shields.io/badge/Generated%20by-CodeBoarding-9cf?style=flat-square)](https://github.com/CodeBoarding/GeneratedOnBoardings)[![Demo](https://img.shields.io/badge/Try%20our-Demo-blue?style=flat-square)](https://www.codeboarding.org/demo)[![Contact](https://img.shields.io/badge/Contact%20us%20-%20contact@codeboarding.org-lightgrey?style=flat-square)](mailto:contact@codeboarding.org)



## Component Details



This component overview describes the core components within the `BeadArrayFiles` subsystem, focusing on their responsibilities in parsing various binary file formats related to bead array data. The main flow involves different parsers utilizing a low-level utility component for basic data reading, with the `GenotypeCallsManager` acting as a central orchestrator integrating data from other parsers.



### BeadArrayUtility

This component provides fundamental utility functions for reading various primitive data types (like bytes, integers, strings, and floats) from file handles and performing basic operations like DNA complement. It acts as a low-level data parsing layer, supporting other components in the BeadArrayFiles subsystem by abstracting the complexities of binary file reading.





**Related Classes/Methods**:



- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadArrayUtility.py#L82-L109" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.BeadArrayUtility.read_string` (82:109)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadArrayUtility.py#L70-L80" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.BeadArrayUtility.read_byte` (70:80)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadArrayUtility.py#L46-L56" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.BeadArrayUtility.read_int` (46:56)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadArrayUtility.py#L58-L68" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.BeadArrayUtility.read_float` (58:68)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadArrayUtility.py#L5-L20" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.BeadArrayUtility.complement` (5:20)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadArrayUtility.py#L34-L44" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.BeadArrayUtility.read_ushort` (34:44)</a>





### BeadPoolManifestParser

This component is responsible for parsing Bead Pool Manifest (BPM) files, which contain crucial information about genetic loci, assay types, and normalization parameters. It orchestrates the reading of the manifest header and individual locus entries, ensuring data integrity and version compatibility.





**Related Classes/Methods**:



- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadPoolManifest.py#L46-L129" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.BeadPoolManifest.BeadPoolManifest.__parse_file` (46:129)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadPoolManifest.py#L236-L368" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.BeadPoolManifest.LocusEntry` (236:368)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadPoolManifest.py#L276-L295" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.BeadPoolManifest.LocusEntry.__parse_file` (276:295)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadPoolManifest.py#L297-L342" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.BeadPoolManifest.LocusEntry.__parse_locus_version_6` (297:342)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadPoolManifest.py#L344-L355" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.BeadPoolManifest.LocusEntry.__parse_locus_version_7` (344:355)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadPoolManifest.py#L357-L368" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.BeadPoolManifest.LocusEntry.__parse_locus_version_8` (357:368)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadPoolManifest.py#L161-L182" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.BeadPoolManifest.SourceStrand.from_string` (161:182)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadPoolManifest.py#L214-L234" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.BeadPoolManifest.RefStrand.from_string` (214:234)</a>





### ClusterFileParser

This component handles the parsing of EGT cluster files, which store clustering information for genotype calls. It reads various sections of the cluster file, including version information, manifest details, and arrays of cluster records and scores, ensuring proper reconstruction of the cluster data.





**Related Classes/Methods**:



- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/ClusterFile.py#L82-L146" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.ClusterFile.ClusterFile.read_cluster_file` (82:146)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/ClusterFile.py#L64-L79" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.ClusterFile.ClusterFile.read_array` (64:79)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/ClusterFile.py#L184-L237" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.ClusterFile.ClusterRecord.read_record` (184:237)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/ClusterFile.py#L270-L284" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.ClusterFile.ClusterScore.read_record` (270:284)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/ClusterFile.py#L2-L146" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.ClusterFile.ClusterFile` (2:146)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/ClusterFile.py#L148-L237" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.ClusterFile.ClusterRecord` (148:237)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/ClusterFile.py#L287-L317" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.ClusterFile.ClusterStats` (287:317)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/ClusterFile.py#L240-L284" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.ClusterFile.ClusterScore` (240:284)</a>





### GenotypeCallsManager

This component is responsible for reading and managing genotype call data from GTC files. It provides a comprehensive interface for accessing various data points such as genotypes, intensities (raw and normalized), scores, and control data, abstracting the underlying file structure.





**Related Classes/Methods**:



- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L103-L136" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.__init__` (103:136)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L155-L182" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.__get_generic_array` (155:182)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L184-L207" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.__get_generic_array_numpy` (184:207)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L299-L304" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.get_genotypes` (299:304)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L306-L346" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.get_base_calls_generic` (306:346)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L348-L361" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.get_base_calls_plus_strand` (348:361)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L363-L375" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.get_base_calls_forward_strand` (363:375)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L377-L408" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.get_base_calls` (377:408)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L410-L415" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.get_genotype_scores` (410:415)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L424-L429" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.get_control_x_intensities` (424:429)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L431-L436" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.get_control_y_intensities` (431:436)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L438-L443" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.get_raw_x_intensities` (438:443)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L445-L450" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.get_raw_y_intensities` (445:450)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L488-L495" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.get_num_calls` (488:495)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L497-L504" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.get_num_no_calls` (497:504)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L506-L513" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.get_num_intensity_only` (506:513)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L515-L523" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.get_ballele_freqs` (515:523)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L525-L533" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.get_logr_ratios` (525:533)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L535-L550" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.get_percentiles_x` (535:550)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L552-L567" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.get_percentiles_y` (552:567)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L569-L581" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.get_normalized_intensities` (569:581)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L583-L588" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.get_normalization_transforms` (583:588)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L590-L621" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.is_write_complete` (590:621)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L223-L228" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.get_ploidy_type` (223:228)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L237-L242" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.GenotypeCalls.get_slide_identifier` (237:242)</a>





### ScannerDataReader

This component is specifically designed to parse and encapsulate scanner-related metadata from file handles. It extracts details such as scanner name, PMT settings, and imaging user, which are typically embedded within genotype call files.





**Related Classes/Methods**:



- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L733-L748" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.ScannerData.read_scanner_data` (733:748)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/GenotypeCalls.py#L700-L748" target="_blank" rel="noopener noreferrer">`BeadArrayFiles.module.GenotypeCalls.ScannerData` (700:748)</a>









### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)
127 changes: 127 additions & 0 deletions .codeboarding/BeadPoolManifest Parser.md
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```mermaid

graph LR

File_Reading_Utilities["File Reading Utilities"]

Bead_Pool_Manifest_Parser["Bead Pool Manifest Parser"]

Locus_Entry_Parser["Locus Entry Parser"]

Strand_Type_Converters["Strand Type Converters"]

Bead_Pool_Manifest_Parser -- "uses" --> File_Reading_Utilities

Bead_Pool_Manifest_Parser -- "creates and uses" --> Locus_Entry_Parser

Locus_Entry_Parser -- "uses" --> File_Reading_Utilities

Locus_Entry_Parser -- "uses" --> Strand_Type_Converters

```

[![CodeBoarding](https://img.shields.io/badge/Generated%20by-CodeBoarding-9cf?style=flat-square)](https://github.com/CodeBoarding/GeneratedOnBoardings)[![Demo](https://img.shields.io/badge/Try%20our-Demo-blue?style=flat-square)](https://www.codeboarding.org/demo)[![Contact](https://img.shields.io/badge/Contact%20us%20-%20contact@codeboarding.org-lightgrey?style=flat-square)](mailto:contact@codeboarding.org)



## Component Details



This subsystem is responsible for parsing Bead Pool Manifest (BPM) files, which contain genetic array data. It comprises several components: `File Reading Utilities` for low-level binary file operations, `Bead Pool Manifest Parser` for orchestrating the overall file parsing, `Locus Entry Parser` for handling individual genetic locus entries, and `Strand Type Converters` for standardizing genetic strand information. The main flow involves the `Bead Pool Manifest Parser` reading the file, utilizing `File Reading Utilities` for basic data extraction, and delegating the parsing of individual locus entries to the `Locus Entry Parser`. The `Locus Entry Parser` further relies on `File Reading Utilities` and `Strand Type Converters` to process detailed genetic information.



### File Reading Utilities

This component provides fundamental utility functions for reading various data types (bytes, integers, strings) from file handles. It serves as a low-level interface for binary file parsing within the BeadArrayFiles subsystem.





**Related Classes/Methods**:



- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadArrayUtility.py#L82-L109" target="_blank" rel="noopener noreferrer">`module.BeadArrayUtility.read_string` (82:109)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadArrayUtility.py#L70-L80" target="_blank" rel="noopener noreferrer">`module.BeadArrayUtility.read_byte` (70:80)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadArrayUtility.py#L46-L56" target="_blank" rel="noopener noreferrer">`module.BeadArrayUtility.read_int` (46:56)</a>





### Bead Pool Manifest Parser

This component is responsible for parsing the overall structure of Bead Pool Manifest (BPM) files. It initializes the manifest object and orchestrates the reading of various sections, including manifest metadata and individual locus entries.





**Related Classes/Methods**:



- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadPoolManifest.py#L21-L44" target="_blank" rel="noopener noreferrer">`module.BeadPoolManifest.BeadPoolManifest.__init__` (21:44)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadPoolManifest.py#L46-L129" target="_blank" rel="noopener noreferrer">`module.BeadPoolManifest.BeadPoolManifest.__parse_file` (46:129)</a>





### Locus Entry Parser

This component handles the parsing of individual locus entries within a Bead Pool Manifest file. It supports different versions of locus entry formats and extracts specific genetic information such as SNPs, chromosomes, and mapping details.





**Related Classes/Methods**:



- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadPoolManifest.py#L254-L274" target="_blank" rel="noopener noreferrer">`module.BeadPoolManifest.LocusEntry.__init__` (254:274)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadPoolManifest.py#L276-L295" target="_blank" rel="noopener noreferrer">`module.BeadPoolManifest.LocusEntry.__parse_file` (276:295)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadPoolManifest.py#L297-L342" target="_blank" rel="noopener noreferrer">`module.BeadPoolManifest.LocusEntry.__parse_locus_version_6` (297:342)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadPoolManifest.py#L344-L355" target="_blank" rel="noopener noreferrer">`module.BeadPoolManifest.LocusEntry.__parse_locus_version_7` (344:355)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadPoolManifest.py#L357-L368" target="_blank" rel="noopener noreferrer">`module.BeadPoolManifest.LocusEntry.__parse_locus_version_8` (357:368)</a>





### Strand Type Converters

This component provides utility functions for converting string representations of genetic strand types (SourceStrand and RefStrand) into their corresponding internal enum-like representations, ensuring consistent data handling.





**Related Classes/Methods**:



- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadPoolManifest.py#L161-L182" target="_blank" rel="noopener noreferrer">`module.BeadPoolManifest.SourceStrand.from_string` (161:182)</a>

- <a href="https://github.com/Illumina/BeadArrayFiles/blob/master/module/BeadPoolManifest.py#L214-L234" target="_blank" rel="noopener noreferrer">`module.BeadPoolManifest.RefStrand.from_string` (214:234)</a>









### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)
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