OpenGene · ivanmilevtues · Jun 16, 2025
diff --git a/.codeboarding/Application Orchestrator.md b/.codeboarding/Application Orchestrator.md
@@ -0,0 +1,149 @@
+```mermaid
+
+graph LR
+
+    Application_Orchestrator["Application Orchestrator"]
+
+    Command_Line_Interface["Command Line Interface"]
+
+    File_Discovery_and_Job_Management["File Discovery and Job Management"]
+
+    Read_Preprocessing_Quality_Control["Read Preprocessing & Quality Control"]
+
+    Debubbling_Algorithm["Debubbling Algorithm"]
+
+    Application_Orchestrator -- "configures using" --> Command_Line_Interface
+
+    Application_Orchestrator -- "manages file processing and parallel execution via" --> File_Discovery_and_Job_Management
+
+    File_Discovery_and_Job_Management -- "delegates data processing to" --> Read_Preprocessing_Quality_Control
+
+    Application_Orchestrator -- "initiates" --> Debubbling_Algorithm
+
+    Read_Preprocessing_Quality_Control -- "consumes output from" --> Debubbling_Algorithm
+
+```
+
+[![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
+
+
+
+The AfterQC pipeline is orchestrated by the Application Orchestrator, which handles command-line argument parsing, discovers FASTQ files for processing, and manages the parallel execution of preprocessing, quality control, and debubbling tasks. It delegates specific functionalities to dedicated components for efficient and modular data analysis.
+
+
+
+### Application Orchestrator
+
+The Application Orchestrator component, embodied by the `after.py` script, serves as the central control unit for the AfterQC pipeline. It is responsible for parsing command-line arguments, discovering input FASTQ files, initiating parallel processing jobs, and coordinating the overall workflow by delegating tasks to the Read Preprocessing & Quality Control and Structural Anomaly Processing components.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/after.py#L13-L92" target="_blank" rel="noopener noreferrer">`after.parseCommand` (13:92)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/after.py#L100-L170" target="_blank" rel="noopener noreferrer">`after.processDir` (100:170)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/after.py#L172-L174" target="_blank" rel="noopener noreferrer">`after.processOptions` (172:174)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/after.py#L176-L183" target="_blank" rel="noopener noreferrer">`after.runDebubble` (176:183)</a>
+
+
+
+
+
+### Command Line Interface
+
+This component is responsible for defining and parsing command-line arguments, allowing users to configure various parameters for the AfterQC tool, such as input/output paths, trimming settings, and quality control thresholds.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/after.py#L13-L92" target="_blank" rel="noopener noreferrer">`after.parseCommand` (13:92)</a>
+
+
+
+
+
+### File Discovery and Job Management
+
+This component automates the discovery of relevant FASTQ files within a specified directory, prepares unique processing options for each identified file set, and manages the creation and execution of multiprocessing jobs to enable parallel processing of sequencing data.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/after.py#L100-L170" target="_blank" rel="noopener noreferrer">`after.processDir` (100:170)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/util.py#L28-L33" target="_blank" rel="noopener noreferrer">`util.parseBool` (28:33)</a>
+
+
+
+
+
+### Read Preprocessing & Quality Control
+
+This component performs the core preprocessing and quality control operations on sequencing data. It applies trimming, assesses base quality, handles barcode sequences, and conducts overlap analysis, generating quality statistics and filtering reads based on user-defined criteria.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/preprocesser.py#L140-L818" target="_blank" rel="noopener noreferrer">`preprocesser.seqFilter` (140:818)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/after.py#L172-L174" target="_blank" rel="noopener noreferrer">`after.processOptions` (172:174)</a>
+
+
+
+
+
+### Debubbling Algorithm
+
+This component implements the debubbling algorithm to identify and remove 'bubble' reads from sequencing data, which are often indicative of sequencing errors or artifacts. It processes input directories to generate and utilize bubble circle information for filtering.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/debubble.py#L35-L52" target="_blank" rel="noopener noreferrer">`debubble.debubbleDir` (35:52)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/after.py#L176-L183" target="_blank" rel="noopener noreferrer">`after.runDebubble` (176:183)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/preprocesser.py#L156-L173" target="_blank" rel="noopener noreferrer">`preprocesser.seqFilter:loadBubbleCircles` (156:173)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/preprocesser.py#L175-L203" target="_blank" rel="noopener noreferrer">`preprocesser.seqFilter:isInBubble` (175:203)</a>
+
+
+
+
+
+
+
+
+
+### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)
diff --git a/.codeboarding/Data I-O & Utilities.md b/.codeboarding/Data I-O & Utilities.md
@@ -0,0 +1,143 @@
+```mermaid
+
+graph LR
+
+    FastqReader["FastqReader"]
+
+    FastqWriter["FastqWriter"]
+
+    SequenceAnalysisUtilities["SequenceAnalysisUtilities"]
+
+    GeneralUtilities["GeneralUtilities"]
+
+    FastqReader -- "provides raw sequence data" --> SequenceAnalysisUtilities
+
+    SequenceAnalysisUtilities -- "processes data from" --> FastqReader
+
+    SequenceAnalysisUtilities -- "provides processed sequence data" --> FastqWriter
+
+    FastqWriter -- "receives data from" --> SequenceAnalysisUtilities
+
+```
+
+[![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
+
+
+
+The Data I/O & Utilities component serves as the foundational layer for handling FASTQ sequencing data within the AfterQC project. It provides robust functionalities for reading and writing FASTQ files, supporting various compression formats. Additionally, it offers a suite of general-purpose and sequence-specific utility functions for data manipulation, quality assessment, and sequence analysis, promoting modularity and reusability across the project's data processing workflows.
+
+
+
+### FastqReader
+
+Manages the reading of FASTQ files, supporting gzipped and bzipped formats. It initializes file handles and provides functionality to iterate through reads. It also includes a utility to check if a file is a FASTQ file.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/fastq.py#L18-L30" target="_blank" rel="noopener noreferrer">`fastq.Reader.__init__` (18:30)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/fastq.py#L36-L48" target="_blank" rel="noopener noreferrer">`fastq.Reader.nextRead` (36:48)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/fastq.py#L50-L51" target="_blank" rel="noopener noreferrer">`fastq.Reader.isEOF` (50:51)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/fastq.py#L6-L11" target="_blank" rel="noopener noreferrer">`fastq.isFastq` (6:11)</a>
+
+
+
+
+
+### FastqWriter
+
+Handles the writing of data to FASTQ files, including support for gzipped output. It provides methods to write individual lines or complete sequence reads and to manage file stream operations like flushing and closing.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/fastq.py#L62-L75" target="_blank" rel="noopener noreferrer">`fastq.Writer.__init__` (62:75)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/fastq.py#L77-L79" target="_blank" rel="noopener noreferrer">`fastq.Writer.flush` (77:79)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/fastq.py#L81-L84" target="_blank" rel="noopener noreferrer">`fastq.Writer.close` (81:84)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/fastq.py#L86-L92" target="_blank" rel="noopener noreferrer">`fastq.Writer.writeLines` (86:92)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/fastq.py#L94-L103" target="_blank" rel="noopener noreferrer">`fastq.Writer.writeRead` (94:103)</a>
+
+
+
+
+
+### SequenceAnalysisUtilities
+
+Provides core utility functions for sequence manipulation and analysis, including calculating edit distances, Hamming distances, determining overlaps using various algorithms, and generating reverse complements. It also includes functions for quality score conversion.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/util.py#L35-L36" target="_blank" rel="noopener noreferrer">`util.complement` (35:36)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/util.py#L38-L39" target="_blank" rel="noopener noreferrer">`util.qualNum` (38:39)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/util.py#L41-L50" target="_blank" rel="noopener noreferrer">`util.reverseComplement` (41:50)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/util.py#L55-L61" target="_blank" rel="noopener noreferrer">`util.hammingDistance` (55:61)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/util.py#L64-L82" target="_blank" rel="noopener noreferrer">`util.editDistance` (64:82)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/util.py#L84-L85" target="_blank" rel="noopener noreferrer">`util.distance_threshold` (84:85)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/util.py#L87-L88" target="_blank" rel="noopener noreferrer">`util.overlap` (87:88)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/util.py#L90-L154" target="_blank" rel="noopener noreferrer">`util.overlap_ed` (90:154)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/util.py#L157-L211" target="_blank" rel="noopener noreferrer">`util.overlap_hm` (157:211)</a>
+
+
+
+
+
+### GeneralUtilities
+
+Contains general-purpose helper functions not specific to sequence data or FASTQ files, such as boolean parsing and string reversal.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/util.py#L28-L33" target="_blank" rel="noopener noreferrer">`util.parseBool` (28:33)</a>
+
+- <a href="https://github.com/OpenGene/AfterQC/blob/master/util.py#L52-L53" target="_blank" rel="noopener noreferrer">`util.reverse` (52:53)</a>
+
+
+
+
+
+
+
+
+
+### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)