Metadata-Version: 2.1
Name: crunchy
Version: 0.1
Summary: Compress fastq with spring
Home-page: https://github.com/Clinical-Genomics/crunchy
Author: Mans Magnusson
Author-email: mans.magnusson@scilifelab.com
License: MIT
Description: 
        [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
        ![Build Status - GitHub](https://github.com/Clinical-Genomics/crunchy/workflows/Build/badge.svg)
        [![codecov](https://codecov.io/gh/Clinical-Genomics/crunchy/branch/master/graph/badge.svg)](https://codecov.io/gh/Clinical-Genomics/crunchy)
        [![CodeFactor](https://www.codefactor.io/repository/github/clinical-genomics/crunchy/badge)](https://www.codefactor.io/repository/github/clinical-genomics/crunchy)
        
        # Crunchy
        
        A python wrapper around [spring][spring] to compress fastq and check the integrity.
        
        ## Install
        
        ```
        git clone https://github.com/Clinical-Genomics/crunchy
        pip install -e .
        crunchy --help
        Usage: crunchy [OPTIONS] COMMAND [ARGS]...
        
          Base command for crunchy
        
        Options:
          --spring-binary TEXT            Path to spring binary  [default: spring]
          -t, --threads INTEGER           Number of threads to use for spring
                                          compression  [default: 8]
          --log-level [DEBUG|INFO|WARNING]
                                          Choose what log messages to show
          --help                          Show this message and exit.
        
        Commands:
          auto        Recursively find all fastq pairs below a directory and spring...
          checksum    Create a checksum for the file(s)
          compress    Compress a file
          decompress  Decompress a file
        ```
        
        ## Workflow
        
        Each command can be run separately. To compress all fastq pairs below a directory run `crunchy auto <path_to_dir>`.
        
        1. **Recursively find all fastq pairs**
        
        1. **Compress all pairs with spring**
        ```file_1.fastq + file_2.fastq (spring)-> file.spring```
        
        1. **Decompress with spring**
        ```file.spring (spring)-> file_1.fastq + file_2.fastq```
        
        1. **Compare checksum with previous**
        ```file_1.fastq + file_2.fastq (hashlib)-> compare```
        
        1. **Delete fastq** (If the compression was lossless)
        ```file_1.fastq + file_2.fastq (rm)->```
        
        [spring]: https://github.com/shubhamchandak94/Spring
Keywords: vcf,compression
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Unix
Classifier: Intended Audience :: Science/Research
Requires-Python: >=3.6.0
Description-Content-Type: text/markdown
