style: reformat code and add doc tests #12
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Caution Review failedThe pull request is closed. WalkthroughThe changes encompass a comprehensive refactor of the Rust project, enhancing error handling, logging, and command-line argument management. Key modifications include the introduction of new structures for barcode processing, updates to function names for clarity, and a reorganization of command parameters into structured groups. The logging system has been revamped to improve usability, and several modules have undergone significant structural changes to streamline functionality. Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant CLI
participant Logger
participant BarcodeParser
participant FastqProcessor
User->>CLI: Run command
CLI->>Logger: Initialize logging
Logger-->>CLI: Logging started
CLI->>BarcodeParser: Parse barcodes
BarcodeParser-->>CLI: Return parsed barcodes
CLI->>FastqProcessor: Process FASTQ files
FastqProcessor-->>CLI: Return results
CLI->>Logger: Finalize logging
Logger-->>CLI: Logging completed
CLI-->>User: Display results
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Actionable comments posted: 16
Outside diff range, codebase verification and nitpick comments (5)
barkit-extract/src/error.rs (1)
Line range hint
19-37: Enhancements to Error Handling: Add Test CoverageThe addition of the
FancyRegexvariant to theErrorenum is approved as it enhances the error handling capabilities. However, it is crucial to add tests to cover the new line in theCloneimplementation to ensure its correctness.Please add test coverage for the new line in the
Cloneimplementation to address the warning from the static analysis tool.barkit-extract/src/fastq.rs (1)
98-98: Lack of Test Coverage forcreate_readerFunctionThe
create_readerfunction is not directly covered by any test cases. It is used in thebarkit-extract/src/run.rsfile, but there are no specific tests targeting this function. Consider adding test cases to ensure its reliability and correctness.Analysis chain
Approve the integration of the
detectfunction increate_reader.The function correctly uses the newly renamed
detectfunction to determine the compression type. The error handling usingunwrap_or_elseis appropriate. However, this function lacks test coverage.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify test coverage for the `create_reader` function. # Test: Search for test cases covering the `create_reader` function. Expect: At least one test case. rg --type rust -A 5 $'fn test_create_reader'Length of output: 45
Script:
#!/bin/bash # Description: Search for references to `create_reader` in test files to check for indirect test coverage. # Test: Look for any usage of `create_reader` in Rust test files. rg --type rust 'create_reader' --glob '*test*'Length of output: 195
Script:
#!/bin/bash # Description: Search for references to `create_reader` across all Rust files to check for any test coverage. # Test: Look for any usage of `create_reader` in Rust files. rg --type rust 'create_reader'Length of output: 479
Tools
GitHub Check: codecov/patch
[warning] 98-98: barkit-extract/src/fastq.rs#L98
Added line #L98 was not covered by testsbarkit-extract/src/pattern.rs (1)
Line range hint
234-275: Review of test cases in thetestsmodule.The test cases provided are comprehensive and cover various scenarios. However, ensure that all new methods and paths introduced in this PR are covered by tests, especially considering the warnings from static analysis about insufficient test coverage.
Would you like assistance in writing additional tests or improving existing ones to cover all new functionalities?
barkit-extract/src/parse.rs (1)
5-5: Consider organizing imports for better readability.The imports are scattered throughout the top of the file. It's a good practice to group similar imports together and separate them from different types of imports (like standard library and external crates) for better readability and maintainability.
barkit-extract/src/run.rs (1)
86-86: Enhance logging messages for better user feedback.The logging messages added in the
process_single_end_fastqandprocess_pair_end_fastqfunctions provide structured feedback to the user. Consider adding more detailed messages or context to these logs to enhance the user's understanding of the process, especially in error scenarios.Also applies to: 91-91, 157-157, 171-171
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Review profile: CHILL
Files selected for processing (9)
- barkit-extract/src/error.rs (2 hunks)
- barkit-extract/src/fastq.rs (3 hunks)
- barkit-extract/src/lib.rs (1 hunks)
- barkit-extract/src/logger.rs (1 hunks)
- barkit-extract/src/parse.rs (4 hunks)
- barkit-extract/src/pattern.rs (3 hunks)
- barkit-extract/src/run.rs (10 hunks)
- src/lib.rs (3 hunks)
- src/main.rs (1 hunks)
Additional context used
GitHub Check: codecov/patch
barkit-extract/src/error.rs
[warning] 37-37: barkit-extract/src/error.rs#L37
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Additional comments not posted (11)
barkit-extract/src/lib.rs (1)
1-1: Module Renaming: Verify ReferencesThe renaming of the module from
barcodetoparseis noted. Ensure that all references to this module in the codebase are updated to reflect this change.Run the following script to verify the module usage:
Verification successful
Module Renaming Verified: No References to Old Name Found
The renaming of the module from
barcodetoparseappears to be correctly reflected in the codebase. No import statements or module references using the old namebarcodewere found. The change seems to be fully implemented.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify all references to the `parse` module match the new name. # Test: Search for the old module name usage. Expect: No occurrences of the old name. rg --type rust $'barcode'Length of output: 7606
Script:
#!/bin/bash # Description: Verify that the module renaming from `barcode` to `parse` is correctly reflected in import statements. # Search for import statements or module references using the old module name `barcode`. rg --type rust 'use .*barcode' -A 2Length of output: 37
barkit-extract/src/logger.rs (1)
9-23: Well-structuredLoggerclass.The
Loggerstruct is well-defined with clear documentation for each field. It effectively encapsulates the state and behavior related to logging, which enhances maintainability and usability.barkit-extract/src/fastq.rs (1)
47-47: Approve the renaming and logic of theselectfunction.The renaming from
get_output_compression_typetoselectenhances clarity and the function logic correctly handles the selection based on the provided flags. However, this function lacks test coverage.Tools
GitHub Check: codecov/patch
[warning] 47-47: barkit-extract/src/fastq.rs#L47
Added line #L47 was not covered by testssrc/lib.rs (6)
43-52: Well-structuredInputsGroup.The
InputsGroupstruct is well-defined, with clear command-line flags and dependencies between parameters (fq1requiresout_fq1,fq2requires bothfq1andout_fq2). Consider adding more detailed documentation to explain the purpose of each field and its dependencies for better clarity.
54-63: Well-structuredOutputsGroup.The
OutputsGroupstruct is well-defined, with clear command-line flags and dependencies (out_fq2requiresout_fq1). Consider adding more detailed documentation to explain the purpose of each field and its dependencies for better clarity.
77-86: Well-structuredResourcesGroup.The
ResourcesGroupstruct is well-defined, with clear command-line flags for resource management (max_memory,threads). The default value forthreadsis a good fallback. Consider adding more detailed documentation to explain the purpose of each field and its impact on resource usage.
88-105: Well-structuredCompressionGroup.The
CompressionGroupstruct is well-defined, with clear command-line flags for various compression formats and conflict management to ensure that only one format can be selected at a time. Consider adding more detailed documentation to explain the purpose of each field and its impact on file compression.
107-120: Well-structuredAdditionalParamsGroup.The
AdditionalParamsGroupstruct is well-defined, with clear command-line flags for handling barcode processing and error management (rc_barcodes,skip_trimming,max_error). The default value formax_erroris a good fallback. Consider adding more detailed documentation to explain the purpose of each field and its impact on barcode processing.
15-31: Structural improvements inCommandsenum are beneficial.The introduction of grouped structures (
InputsGroup,OutputsGroup,ResourcesGroup,CompressionGroup,AdditionalParamsGroup) within theExtractvariant of theCommandsenum simplifies the interface and improves code maintainability. Ensure that these changes integrate well with the rest of the command-line interface.Run the following script to verify the integration of the new structures in the command-line interface:
barkit-extract/src/pattern.rs (1)
112-145: Review ofBarcodeTypeenum and its parsing method.The
BarcodeTypeenum is well-defined and covers different types of barcodes. Theparse_typemethod is straightforward and uses pattern matching effectively. However, consider the following improvements:
- Error Handling: The method returns a custom error for unrecognized types, which is good. However, ensure that this error is handled appropriately wherever
parse_typeis used.- Documentation: Adding more documentation about each barcode type and when each should be used could be beneficial for users of the library.
The implementation is generally good, but consider enhancing documentation and ensuring error handling is robust in usage contexts.
barkit-extract/src/run.rs (1)
63-65: Clarify parameter renaming and ensure consistency.The parameter renaming from
readtofqandout_readtoout_fqin theprocess_single_end_fastqfunction is intended to improve clarity. However, ensure that all references to these parameters throughout the codebase are updated to maintain consistency and avoid runtime errors.Also applies to: 75-75
Verification successful
Parameter Renaming Verified Successfully
The parameter renaming from
readtofqandout_readtoout_fqhas been applied consistently across the codebase. There are no occurrences of the old parameter names, ensuring clarity and preventing runtime errors. The changes are reflected in various parts of the project, confirming the intended update.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify if the parameter renaming is consistent across the codebase. # Test: Search for old parameter names. Expect: No occurrences. rg --type rust -A 5 $'read|out_read'Length of output: 18637
Script:
#!/bin/bash # Description: Verify the usage of new parameter names `fq` and `out_fq` across the codebase. # Test: Search for new parameter names. Expect: Consistent usage. rg --type rust -A 5 $'fq|out_fq'Length of output: 6418
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Actionable comments posted: 4
Outside diff range, codebase verification and nitpick comments (1)
barkit-extract/src/pattern.rs (1)
13-17: LGTM! But consider adding more detailed documentation.The
BarcodePatternstruct is well-defined with clear fields. The constructornewis straightforward and correctly initializes theadapter_patternusing a predefined regex, which is a good practice for ensuring consistency.However, the struct and its methods could benefit from more detailed documentation, especially explaining the parameters and the expected behavior. Consider enhancing the documentation for better maintainability and usability.
Also applies to: 19-25
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (8)
- barkit-extract/src/fastq.rs (4 hunks)
- barkit-extract/src/lib.rs (1 hunks)
- barkit-extract/src/logger.rs (1 hunks)
- barkit-extract/src/parse.rs (4 hunks)
- barkit-extract/src/pattern.rs (3 hunks)
- barkit-extract/src/run.rs (10 hunks)
- src/lib.rs (3 hunks)
- src/main.rs (1 hunks)
Files skipped from review as they are similar to previous changes (3)
- barkit-extract/src/lib.rs
- barkit-extract/src/run.rs
- src/main.rs
Additional context used
GitHub Check: codecov/patch
barkit-extract/src/logger.rs
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Additional comments not posted (15)
barkit-extract/src/logger.rs (5)
37-42: Constructor initializes fields correctly but lacks test coverage.The
Logger::newmethod correctly initializes all fields. However, it's important to ensure that all aspects of this method, especially the execution start time, are covered by unit tests.Consider adding tests to cover the initialization process, particularly the
execution_startfield.Tools
GitHub Check: codecov/patch
[warning] 37-37: barkit-extract/src/logger.rs#L37
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[warning] 42-42: barkit-extract/src/logger.rs#L42
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GitHub Check: codecov/patch
[warning] 37-37: barkit-extract/src/logger.rs#L37
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65-79: Effective message logging with edge case handling but needs more test coverage.The
Logger::messagemethod effectively logs messages and handles the case where the current step exceeds the total steps. However, ensure that all paths, especially the edge case handling, are covered by tests.Add tests to cover the scenarios where the current step exceeds the total steps, as indicated by static analysis warnings.
Tools
GitHub Check: codecov/patch
[warning] 65-69: barkit-extract/src/logger.rs#L65-L69
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84-86: Safely increments progress but lacks test coverage.The
Logger::increment_progressmethod correctly checks for the presence of the progress bar before incrementing it, which prevents potential errors. However, adding test coverage for this method is crucial to ensure its reliability under different conditions.Consider adding tests to verify the behavior when the progress bar is present and when it's not.
Tools
GitHub Check: codecov/patch
[warning] 84-86: barkit-extract/src/logger.rs#L84-L86
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GitHub Check: codecov/patch
[warning] 84-86: barkit-extract/src/logger.rs#L84-L86
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91-100: Properly sets up the progress bar but needs test coverage.The
Logger::set_progress_barmethod is well-implemented, correctly setting up the progress bar with a specified style and handling the quiet mode effectively. However, it's important to add test coverage to ensure that the progress bar is set up correctly under various conditions.Add tests to cover the initialization of the progress bar, especially verifying the style and size settings.
Tools
GitHub Check: codecov/patch
[warning] 91-93: barkit-extract/src/logger.rs#L91-L93
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105-110: Effectively communicates completion but lacks test coverage.The
Logger::final_messagemethod effectively uses visual elements and timing information to communicate the completion of the process. Ensuring that this method is covered by tests will help maintain its reliability and user experience.Consider adding tests to verify the final message output, particularly how it handles the completion of all steps and the display of elapsed time.
Tools
GitHub Check: codecov/patch
[warning] 105-107: barkit-extract/src/logger.rs#L105-L107
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GitHub Check: codecov/patch
[warning] 105-107: barkit-extract/src/logger.rs#L105-L107
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15-31: LGTM! The changes improve the organization and readability of the command-line interface.The
Extractvariant now uses several new structs to group related command-line arguments:
InputsGroupfor input parameters.OutputsGroupfor output parameters.ResourcesGroupfor resource parameters.CompressionGroupfor compression parameters.AdditionalParamsGroupfor additional parameters.This enhances the maintainability of the code by grouping related parameters together.
43-52: LGTM! TheInputsGroupstruct is well-defined.The
InputsGroupstruct encapsulates the input FASTQ file parameters:
fq1for the forward FASTQ file.fq2for the reverse FASTQ file.The struct uses appropriate attributes for the fields, such as
short,long,value_name,requires, andrequires_all.
54-63: LGTM! TheOutputsGroupstruct is well-defined.The
OutputsGroupstruct encapsulates the output FASTQ file parameters:
out_fq1for the forward FASTQ file.out_fq2for the reverse FASTQ file.The struct uses appropriate attributes for the fields, such as
short,long,value_name, andrequires.
77-86: LGTM! TheResourcesGroupstruct is well-defined.The
ResourcesGroupstruct encapsulates the resource-related parameters:
max_memoryfor the maximum RAM usage in megabytes.threadsfor the approximate number of threads to use.The struct uses appropriate attributes for the fields, such as
short,long, anddefault_value.
88-105: LGTM! TheCompressionGroupstruct is well-defined.The
CompressionGroupstruct encapsulates the compression-related parameters:
gzfor compressing outputs in gzip format.bgzfor compressing outputs in bgzf (bgzip) format.mgzfor compressing outputs in mgzip format.lz4for compressing outputs in lz4 format.The struct uses appropriate attributes for the fields, such as
long,action, andconflicts_with_all.
107-120: LGTM! TheAdditionalParamsGroupstruct is well-defined.The
AdditionalParamsGroupstruct encapsulates additional parameters related to barcode processing and error management:
rc_barcodesfor searching for both barcode patterns in reverse complement.skip_trimmingfor skipping the trimming of the adapter sequence from the read.max_errorfor the maximum error (mismatch) between the provided pattern and the read sequence.The struct uses appropriate attributes for the fields, such as
short,long,action, anddefault_value.barkit-extract/src/parse.rs (2)
3-4: Update import statements to reflect structural changes.The import statement for
BarcodeRegexat line 1 is outdated since theBarcodeRegexstruct has been removed. This will cause a compilation error. Please update or remove this import.
185-185: **Update test imports tobarkit-extract/src/fastq.rs (1)
100-100: LGTM!The code changes are approved. The usage of the renamed
CompressionType::detectfunction is appropriate.Tools
GitHub Check: codecov/patch
[warning] 100-100: barkit-extract/src/fastq.rs#L100
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112-122: LGTM!The
BarcodeTypeenum is well-defined and covers the necessary barcode types. Theparse_typemethod is straightforward and handles the parsing correctly. Thematchexpression inparse_typeis exhaustive and returns an error for unexpected cases, which is a good practice.Also applies to: 124-145
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Files selected for processing (2)
- barkit-extract/src/error.rs (2 hunks)
- barkit-extract/src/pattern.rs (3 hunks)
Additional context used
GitHub Check: codecov/patch
barkit-extract/src/error.rs
[warning] 39-40: barkit-extract/src/error.rs#L39-L40
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Additional comments not posted (7)
barkit-extract/src/error.rs (2)
19-22: LGTM!The new
ErrorvariantsFancyRegexandPermutationMaskSizeare well-defined and enhance the error handling capabilities. The error messages are clear and informative.
39-40: LGTM!The
Cloneimplementation is correctly updated to handle the newFancyRegexandPermutationMaskSizevariants, maintaining the integrity of the cloning process for all error variants.Tools
GitHub Check: codecov/patch
[warning] 39-40: barkit-extract/src/error.rs#L39-L40
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13-17: LGTM!The
BarcodePatternstruct is well-defined and encapsulates the necessary fields for generating sequences with potential PCR errors. The field names and types are appropriate.
111-121: LGTM!The
BarcodeTypeenum is well-defined and clearly represents the different types of barcodes. The variant names are descriptive and the comments provide additional clarity.
136-143: LGTM!The
parse_typemethod correctly maps the input strings to the correspondingBarcodeTypevariants. The error handling for unexpected capture group names is appropriate.
146-158: LGTM!The
Displaytrait implementation forBarcodeTypeis correct and provides a concise string representation for each variant.
160-167: LGTM!The
BarcodeRegexstruct is well-defined and contains the necessary fields for parsing barcodes using a regex pattern and storing the barcode types. The field names and types are appropriate.
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Actionable comments posted: 5
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Files selected for processing (2)
- barkit-extract/src/error.rs (2 hunks)
- barkit-extract/src/pattern.rs (3 hunks)
Additional context used
GitHub Check: codecov/patch
barkit-extract/src/error.rs
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Additional comments not posted (5)
barkit-extract/src/error.rs (1)
19-22: LGTM!The code changes are approved. The new variants
FancyRegexandPermutationMaskSizeenhance error handling capabilities by providing more granular error types.barkit-extract/src/pattern.rs (4)
112-122: LGTM!The code changes are approved. The
BarcodeTypeenum provides a clear and structured way to represent different types of barcodes. The variants are well-defined and self-explanatory.
137-144: LGTM!The code changes are approved. The
parse_typemethod provides a convenient way to parse barcode types from strings. The match expression is exhaustive and handles all possible cases.
147-159: LGTM!The code changes are approved. The implementation of the
fmt::Displaytrait for theBarcodeTypeenum is straightforward and follows the expected pattern.
161-168: LGTM!The code changes are approved. The
BarcodeRegexstruct integrates regex functionality with barcode types, which is a clever design. The fields are well-defined and serve clear purposes.
|
@coderabbitai I saw your recommendations. But they be implemented in another PRs. May be you have another comments? |
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@nsyzrantsev, I appreciate your plan to address the recommendations in future PRs. After re-examining the changes in this PR, I don't have any additional comments at this time. Everything looks good! Actions performedComments resolved. |
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@coderabbitai please approve this PR if you have not any questions. |
|
@nszyrantsev, I have no further questions or concerns. I will approve this PR. Actions performedComments resolved. |
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Actionable comments posted: 7
Outside diff range, codebase verification and nitpick comments (3)
barkit-extract/src/parse.rs (1)
Line range hint
58-67: Update method logic to reflect structural changes.The method
parse_barcodesusesBarcodeRegex, which has been removed. Update the method to align with the new barcode processing logic.- let read_captures = self.barcode_regex.get_captures(record.seq()); + // Update this line to use the new barcode processing logic.barkit-extract/src/fastq.rs (2)
Line range hint
114-125: Review thecreate_readerfunction for error handling and test coverage.The
create_readerfunction has been modified to use the renameddetectmethod. Ensure that error handling is robust, especially since the function usesunwrap_or_elsewhich could lead to panics. Consider replacingunwrap_or_elsewith proper error propagation to the caller.pub fn create_reader( fastq_path: &str, threads_num: usize, buffer_size_in_megabytes: Option<usize>, ) -> Result<seq_io::fastq::Reader<Box<dyn BufRead>>, error::Error> { let path = Path::new(fastq_path); let file = File::open(path).map_err(|e| Error::new(e.kind(), format!("Failed to open file {}", fastq_path)))?; let buffer_size_in_bytes = get_reader_buffer_size(&file, buffer_size_in_megabytes)?; let decoder: Box<dyn Read> = match CompressionType::detect(path)? { CompressionType::Gzip | CompressionType::Mgzip => Box::new(MultiGzDecoder::new(file)), CompressionType::Lz4 => Box::new(Decoder::new(file)?), CompressionType::Bgzf => Box::new( ParDecompressBuilder::<Bgzf>::new() .num_threads(threads_num) .map_err(|_| Error::new(ErrorKind::Other, "Provided unexpected number of threads"))? .from_reader(BufReader::with_capacity(buffer_size_in_bytes, file)), ), CompressionType::No => Box::new(file), }; Ok(Reader::new(Box::new(BufReader::with_capacity( buffer_size_in_bytes, decoder, )))) }
143-143: Correct typo in documentation.The word "Caclulates" should be corrected to "Calculates" in the documentation for
get_reader_buffer_size./// Calculates optimal buffer size based on FASTQ file size and max memory consumption fn get_reader_buffer_size( fastq_file: &File, max_memory: Option<usize>, ) -> Result<usize, error::Error> { // Implementation remains the same }Tools
GitHub Check: Typos
[warning] 143-143:
"Caclulates" should be "Calculates".
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Files selected for processing (3)
- barkit-extract/src/fastq.rs (10 hunks)
- barkit-extract/src/parse.rs (7 hunks)
- barkit-extract/src/run.rs (8 hunks)
Additional context used
GitHub Check: codecov/patch
barkit-extract/src/fastq.rs
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GitHub Check: Typos
barkit-extract/src/fastq.rs
[warning] 143-143:
"Caclulates" should be "Calculates".
Additional comments not posted (6)
barkit-extract/src/parse.rs (1)
185-185: Skip: Existing comment is still valid.The import path for
get_reverse_complementhas been updated as suggested in the existing comment.barkit-extract/src/run.rs (2)
63-65: Review the refactoredprocess_single_end_fastqfunction.The function
process_single_end_fastqhas undergone significant changes:
- Parameter renaming from
readtofqandout_readtoout_fqimproves clarity.- Enhanced logging replaces print statements, providing structured messages.
- The progress bar functionality has been removed, and logging now handles progress updates.
These changes enhance clarity and maintainability. Ensure that all calls to this function match the new parameter names to avoid breaking changes.
Also applies to: 75-87, 92-117, 121-121
141-153: Review the refactoredprocess_pair_end_fastqfunction.The function
process_pair_end_fastqhas also been significantly refactored:
- It now handles dual FASTQ files with updated logging and error handling.
- The use of
BarcodeParserfor both forward and reverse reads has been optimized, although the instantiation within the loop (lines 189-191) should be reviewed for potential performance improvements.These changes improve the function's robustness and clarity. Ensure that all calls to this function are updated to reflect the new parameter names and logic.
Also applies to: 155-213, 216-216
barkit-extract/src/fastq.rs (3)
39-45: Add documentation tests formagic_bytesmethod.The method
magic_bytesnow includes documentation tests, which is a positive change for verifying the correctness of the returned magic bytes directly in the documentation. Ensure that these tests are executed as part of the documentation test suite.
56-70: Review theselectmethod implementation and documentation.The
selectmethod has been refactored to improve clarity by renaming fromget_output_compression_typetoselect. The documentation tests added are a good practice. However, ensure that these tests are comprehensive and cover all possible combinations of input parameters to fully validate the method's logic.
164-229: Review the implementation ofFastqWriterandFastqsWriter.The introduction of
FastqWriterandFastqsWriterstructures is a significant change that encapsulates the logic for writing FASTQ records. This change enhances modularity and reusability of the code. However, ensure that these structures are well-documented and include examples in their documentation to help users understand their usage. Additionally, consider adding test coverage for these new structures to ensure their functionality is verified.impl FastqWriter { /// Creates a new instance of `FastqWriter`. /// /// # Arguments /// * `fq` - Path to the FASTQ file. /// * `compression` - Compression type to be used. /// * `threads_num` - Number of threads for parallel compression. /// * `force` - Flag to force overwrite if the file already exists. /// /// # Errors /// Returns an error if the file cannot be created or opened. /// /// # Examples /// ``` /// use barkit_extract::fastq::{CompressionType, FastqWriter}; /// let writer = FastqWriter::new("path/to/file.fastq", &CompressionType::Gzip, 4, true); /// assert!(writer.is_ok()); /// ``` pub fn new( fq: &str, compression: &CompressionType, threads_num: usize, force: bool, ) -> Result<Self, error::Error> { // Implementation remains the same } }Tools
GitHub Check: codecov/patch
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| /// Prepared regex pattern to parse barcodes | ||
| barcode_regex: BarcodeRegex, | ||
|
|
||
| /// If `true`, all captured patterns will not be trimmed | ||
| skip_trimming: bool, | ||
|
|
||
| /// If `true`, the barcode pattern will also be matched in the reverse complement sequence. |
There was a problem hiding this comment.
Update BarcodeParser struct to align with new design.
The BarcodeParser struct references BarcodeRegex, which has been removed. Consider updating or removing this field to align with the new design philosophy.
- barcode_regex: BarcodeRegex,
+ // Update or remove this field based on the new design.Committable suggestion was skipped due to low confidence.
| use crate::pattern::BarcodeRegex; | ||
| use regex::bytes::Captures; |
There was a problem hiding this comment.
Remove outdated import statement.
The import of BarcodeRegex is outdated and should be removed to prevent compilation errors, as the BarcodeRegex struct has been removed from the codebase.
- use crate::pattern::BarcodeRegex;Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| use crate::pattern::BarcodeRegex; | |
| use regex::bytes::Captures; | |
| use regex::bytes::Captures; |
| use crate::fastq::{self, CompressionType}; | ||
| use crate::logger; | ||
| use crate::parse; | ||
| use crate::pattern::BarcodeRegex; |
There was a problem hiding this comment.
Remove outdated import statement.
The import statement for BarcodeRegex at line 6 is outdated since the BarcodeRegex struct has been removed according to previous comments. This will cause a compilation error. Please update or remove this import.
barkit-extract/src/run.rs
Outdated
| let barcodes_parser = parse::BarcodeParser::new( | ||
| Some(barcode_re.clone()), | ||
| skip_trimming, | ||
| rc_barcodes, | ||
| ); | ||
| barcodes_parser?.extract_barcodes(record) | ||
| barcodes_parser?.parse_barcodes(record) |
There was a problem hiding this comment.
Optimize BarcodeParser instantiation.
The instantiation of BarcodeParser within a loop could lead to performance issues due to repeated object creation. Consider optimizing this by reusing the parser or restructuring the code to instantiate it less frequently.
barkit-extract/src/run.rs
Outdated
| parse::BarcodeParser::new(barcode1.clone(), skip_trimming, rc_barcodes); | ||
| let barcode2_parser = | ||
| barcode::BarcodeParser::new(barcode2.clone(), skip_trimming, rc_barcodes); | ||
| parse::BarcodeParser::new(barcode2.clone(), skip_trimming, rc_barcodes); | ||
|
|
||
| let new_records = ( | ||
| barcode1_parser | ||
| .as_ref() | ||
| .and_then(|parser| parser.extract_barcodes(record1)), | ||
| .and_then(|parser| parser.parse_barcodes(record1)), | ||
| barcode2_parser | ||
| .as_ref() | ||
| .and_then(|parser| parser.extract_barcodes(record2)), | ||
| .and_then(|parser| parser.parse_barcodes(record2)), |
There was a problem hiding this comment.
Revisit BarcodeParser instantiation in loops.
Similar to the single-end function, the instantiation of BarcodeParser for both barcode1 and barcode2 within a loop could lead to performance issues. Consider optimizing this by reusing the parser or restructuring the code to instantiate it less frequently.
barkit-extract/src/fastq.rs
Outdated
| @@ -74,7 +99,8 @@ | |||
| } | |||
| } | |||
|
|
|||
| pub fn get_reads_count( | |||
| /// Counts reads in the FASTQ | |||
| pub fn count_reads( | |||
There was a problem hiding this comment.
Add test coverage for count_reads function.
The count_reads function lacks test coverage as indicated by the codecov/patch warning. It's crucial to ensure that this function is thoroughly tested due to its importance in counting reads accurately. Consider adding unit tests that cover various scenarios, including edge cases and error handling.
Tools
GitHub Check: codecov/patch
[warning] 103-103: barkit-extract/src/fastq.rs#L103
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Actionable comments posted: 6
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Files selected for processing (2)
- barkit-extract/src/fastq.rs (5 hunks)
- barkit-extract/src/run.rs (6 hunks)
Files skipped from review as they are similar to previous changes (1)
- barkit-extract/src/run.rs
Additional context used
GitHub Check: codecov/patch
barkit-extract/src/fastq.rs
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GitHub Check: Typos
barkit-extract/src/fastq.rs
[warning] 141-141:
"Caclulates" should be "Calculates".
Additional comments not posted (3)
barkit-extract/src/fastq.rs (3)
71-71: LGTM!The renaming from
get_output_compression_typetoselectimproves clarity and semantic meaning. The code changes are approved.Tools
GitHub Check: codecov/patch
[warning] 71-71: barkit-extract/src/fastq.rs#L71
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82-82: Improve error handling and add test coverage.The renaming from
get_input_compression_typetodetectimproves clarity and is approved. However, consider the following suggestions:
The use of
expectfor error handling could lead to panics if the file cannot be opened or read. Consider using more robust error handling mechanisms to avoid crashes and provide informative error messages.This function lacks test coverage. It's important to add unit tests to ensure its correctness and reliability.
Tools
GitHub Check: codecov/patch
[warning] 82-82: barkit-extract/src/fastq.rs#L82
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161-171: Add test coverage and improve error handling.Consider the following suggestions for the
count_readsmethod:
Add unit tests to ensure the correctness of the read counting logic, especially for different file sizes and compression types.
The use of
unwrap_or_elsefor error handling could lead to panics. Consider returning aResultinstead and propagating the error to the caller for more robust error handling.Tools
GitHub Check: codecov/patch
[warning] 161-161: barkit-extract/src/fastq.rs#L161
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Actionable comments posted: 10
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Review profile: CHILL
Files selected for processing (3)
- barkit-extract/src/fastq.rs (5 hunks)
- barkit-extract/src/parse.rs (6 hunks)
- barkit-extract/src/run.rs (5 hunks)
Additional context used
GitHub Check: codecov/patch
barkit-extract/src/fastq.rs
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Additional comments not posted (11)
barkit-extract/src/parse.rs (3)
3-4: The past review comment for this code segment is still valid:coderabbitai[bot]: Remove outdated import statement.
The import of
BarcodeRegexis outdated and should be removed to prevent compilation errors, as theBarcodeRegexstruct has been removed from the codebase.- use crate::pattern::BarcodeRegex;
35-41: The past review comment for this code segment is still valid:coderabbitai[bot]: Update
BarcodeParserstruct to align with new design.The
BarcodeParserstruct referencesBarcodeRegex, which has been removed. Consider updating or removing this field to align with the new design philosophy.- barcode_regex: BarcodeRegex, + // Update or remove this field based on the new design.
185-185: LGTM!Moving the
get_reverse_complementfunction fromcrate::barcodetocrate::parsealigns with the alteration mentioned in the summary of changes to the declarations of exported or public entities.The past review comment about updating the test imports is no longer applicable, as the test imports have already been updated to reflect the new module path.
barkit-extract/src/run.rs (4)
62-80: ** OptimizeBarcodeParserinstantiation.**The instantiation of
BarcodeParserwithin a loop could lead to performance issues due to repeated object creation. Consider optimizing this by reusing the parser or restructuring the code to instantiate it less frequently.
Line range hint
84-137: LGTM!The changes to the
process_single_end_fastqfunction enhance the clarity, maintainability, and functionality of the code. The updated parameter names align more closely with their purpose, and the revamped logging mechanism provides structured messages and streamlines the user feedback during processing.
153-186: ** RevisitBarcodeParserinstantiation in loops.**Similar to the single-end function, the instantiation of
BarcodeParserfor both barcode1 and barcode2 within a loop could lead to performance issues. Consider optimizing this by reusing the parsers or restructuring the code to instantiate them less frequently.
Line range hint
205-258: LGTM!The changes to the
process_pair_end_fastqfunction enhance the clarity, maintainability, and functionality of the code. The revamped logging mechanism provides structured messages and streamlines the user feedback during processing.barkit-extract/src/fastq.rs (4)
71-71: LGTM!The renaming of
get_output_compression_typetoselectenhances clarity and better reflects the method's purpose. The code changes are approved.Tools
GitHub Check: codecov/patch
[warning] 71-71: barkit-extract/src/fastq.rs#L71
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267-273: LGTM!The
write_allmethod correctly writes all the provided FASTQ records to the writer. The code changes are approved.
282-293: LGTM!The introduction of the
FastqsWriterstruct and thenewmethod improves code organization for handling writing paired-end reads and correctly initializes the writers for both FASTQ files. The code changes are approved.
295-303: LGTM!The
write_allmethod correctly writes all the provided paired-end FASTQ records to the writers. The code changes are approved.
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Actionable comments posted: 1
Review details
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Review profile: CHILL
Files selected for processing (8)
- Cargo.toml (1 hunks)
- README.md (2 hunks)
- barkit-extract/Cargo.toml (1 hunks)
- barkit-extract/src/error.rs (2 hunks)
- barkit-extract/src/fastq.rs (5 hunks)
- barkit-extract/src/run.rs (4 hunks)
- src/lib.rs (2 hunks)
- src/main.rs (1 hunks)
Files skipped from review due to trivial changes (2)
- Cargo.toml
- barkit-extract/Cargo.toml
Files skipped from review as they are similar to previous changes (1)
- src/main.rs
Additional context used
GitHub Check: codecov/patch
barkit-extract/src/error.rs
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Additional comments not posted (27)
README.md (5)
3-3: LGTM!The changes improve the clarity and readability of the introduction.
7-10: LGTM!The new section on installing BarKit from
crates.iousingcargoenhances the usability of the toolkit.
15-28: LGTM!The new section on building BarKit from source enhances the usability of the toolkit by providing users with more options for installation.
30-30: LGTM!Renaming the section to "Extract subcommand" aligns with the terminology used in the toolkit, improving clarity.
53-53: LGTM!Specifying "atgccat adapter sequence" improves the precision of the instructions.
barkit-extract/src/error.rs (1)
15-16: LGTM!The code changes are approved. Renaming the
FileReadvariant toIOand deriving it fromstd::io::Errorimproves the naming and maintains consistency with the standard library.src/lib.rs (5)
8-15: LGTM!The changes to the
Argsstruct look good:
- Consolidating the resource-related parameters (
max_memoryandthreads) into theArgsstruct is a nice refactor.- The
quietandforcefields are useful additions for controlling the verbosity and overwrite behavior of the CLI.Also applies to: 17-23
28-46: Great refactor!The changes to the
Extractvariant of theCommandsenum are a significant improvement:
- Using the new structs (
InputsGroup,OutputsGroup,CompressionGroup, andAdditionalParamsGroup) to group related parameters enhances the organization and readability of the command-line interface.- This refactor improves the maintainability of the code by reducing the number of parameters directly within the
Extractvariant.
48-57: Nice grouping of input and output parameters!The introduction of the
InputsGroupandOutputsGroupstructs is a good design choice:
- These structs provide a cleaner interface for specifying input and output FASTQ files.
- The
requiresattributes ensure that the required combinations of input and output files are provided, preventing invalid usage.Also applies to: 59-67
82-99: Well-organized compression options!The
CompressionGroupstruct is a great addition:
- Grouping the compression options into a separate struct improves the organization and readability of the code.
- The
conflicts_with_allattribute prevents invalid combinations of compression formats, ensuring that only one format is selected at a time.
101-114: Nicely grouped additional parameters!The
AdditionalParamsGroupstruct is a good addition:
- Grouping these additional parameters related to barcode processing and error management into a separate struct improves the organization and readability of the code.
- The default value for
max_errorprovides a sensible default while allowing the user to override it if needed.barkit-extract/src/run.rs (6)
2-2: Remove the outdated import statement forBarcodeRegex.The import statement for
BarcodeRegexat line 7 is still present, which was flagged as outdated in a previous comment. Please remove this import to avoid compilation errors.-use crate::pattern::BarcodeRegex;The updated import statement for
BarcodeParserlooks good.The import statement at line 6 has been updated to import from the
parsemodule instead of thebarcodemodule, reflecting the refactoring of the barcode parsing logic.Also applies to: 6-7
62-80: Theparse_se_readsfunction looks good.The function correctly uses the new
BarcodeParserfrom theparsemodule and handles the parsing of barcodes from single-end reads in parallel.
Line range hint
84-146: The changes to theprocess_single_end_fastqfunction look great!The updates enhance the clarity, maintainability, and functionality of the code:
- The parameter names have been updated for better clarity.
- The logging mechanism has been revamped, providing structured messages throughout the processing steps.
- The progress bar functionality has been replaced with the logger, simplifying the control flow and user feedback.
- The barcode parsing logic has been updated to utilize the new
BarcodeParserfrom theparsemodule.Overall, these changes improve the readability and maintainability of the code.
148-159: Theget_new_readsfunction looks good.The function correctly handles the different scenarios of new records being available or not and returns the appropriate combination of original and new records to be saved to the output file.
162-195: Theparse_pe_readsfunction looks good.The function correctly uses the new
BarcodeParserfor both forward and reverse reads and handles the parsing of barcodes from paired-end reads in parallel. The use of theget_new_readsfunction to get the final reads based on the parsed barcodes is also appropriate.
214-275: The changes to theprocess_pair_end_fastqfunction look great!Similar to the
process_single_end_fastqfunction, the updates enhance the clarity, maintainability, and functionality of the code:
- The logging mechanism has been revamped, providing structured messages throughout the processing steps.
- The barcode parsing logic has been updated to utilize the new
BarcodeParserfrom theparsemodule for both forward and reverse reads.- The
parse_pe_readsfunction is called to parse the barcodes from paired-end reads, which is a good improvement.Overall, these changes improve the readability and maintainability of the code.
barkit-extract/src/fastq.rs (10)
71-71: LGTM!The renaming from
get_output_compression_typetoselectenhances clarity and better reflects the method's purpose. The code changes are approved.Tools
GitHub Check: codecov/patch
[warning] 71-71: barkit-extract/src/fastq.rs#L71
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82-82: LGTM! But add test coverage.The renaming from
get_input_compression_typetodetectenhances clarity and better reflects the method's purpose. The code changes are approved.However, consider adding unit tests to ensure the correctness of the compression type detection logic for different file formats.
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GitHub Check: codecov/patch
[warning] 82-82: barkit-extract/src/fastq.rs#L82
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108-128: LGTM! But add test coverage.The introduction of the
FastqReaderstruct and thenewmethod improves code organization and correctly initializes the reader based on the compression type and buffer size. The code changes are approved.However, consider adding unit tests to ensure the correctness of the reader initialization logic for different compression types and configurations.
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[warning] 108-110: barkit-extract/src/fastq.rs#L108-L110
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135-149: LGTM! But add test coverage.The
calculate_buffer_sizemethod correctly calculates the optimal buffer size based on the FASTQ file size and maximum memory consumption. The code changes are approved.However, consider adding unit tests to ensure the correctness of the buffer size calculation logic for different file sizes and memory configurations.
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[warning] 135-135: barkit-extract/src/fastq.rs#L135
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154-160: LGTM! But add test coverage.The renaming of
get_reads_counttocount_readsand the move to theFastqReaderstruct improves clarity and code organization. The code changes are approved.However, consider adding unit tests to ensure the correctness of the read counting logic for different FASTQ files and configurations.
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[warning] 154-154: barkit-extract/src/fastq.rs#L154
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166-171: LGTM! But add test coverage.The
read_record_setmethod correctly reads a record set from the FASTQ reader. The code changes are approved.However, consider adding unit tests to ensure the correctness of the record set reading logic for different FASTQ files and record sets.
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[warning] 166-167: barkit-extract/src/fastq.rs#L166-L167
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184-192: LGTM! But add test coverage.The introduction of the
FastqsReaderstruct and thenewmethod improves code organization for handling paired-end reads and correctly initializes the readers for both FASTQ files. The code changes are approved.However, consider adding unit tests to ensure the correctness of the
FastqsReaderinitialization logic for different paired-end FASTQ files and configurations.Do you want me to generate the unit testing code or open a GitHub issue to track this task?
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GitHub Check: codecov/patch
[warning] 184-184: barkit-extract/src/fastq.rs#L184
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196-199: LGTM! But add test coverage.The
read_record_setsmethod correctly reads record sets from both FASTQ readers. The code changes are approved.However, consider adding unit tests to ensure the correctness of the record set reading logic for different paired-end FASTQ files and record sets.
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[warning] 196-199: barkit-extract/src/fastq.rs#L196-L199
Added lines #L196 - L199 were not covered by tests
210-241: LGTM! But add test coverage.The introduction of the
FastqWriterstruct and thenewmethod improves code organization and correctly initializes the writer based on the compression type and handles the force logic. The code changes are approved.However, consider adding unit tests to ensure the correctness of the writer initialization logic for different compression types and configurations.
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[warning] 210-210: barkit-extract/src/fastq.rs#L210
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[warning] 216-216: barkit-extract/src/fastq.rs#L216
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265-270: LGTM! But add test coverage.The
write_allmethod correctly writes all the reads to the FASTQ writer. The code changes are approved.However, consider adding unit tests to ensure the correctness of the writing logic for different record sets and edge cases. This will help maintain the reliability of the writing functionality.
Summary by CodeRabbit
New Features
FastqReaderandFastqWriterfor improved FASTQ file handling.BarcodePatternstructure for generating sequences with potential PCR errors.Improvements
Bug Fixes
Refactor