Metadata-Version: 2.1
Name: crunchy
Version: 0.3
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] and cram (samtools) to compress fastq to spring and bam to cram. When compressing fastqs to spring an integrity check can be performed by using flag: `crunchy compress spring --spring-path <springfile> --first <read_1.fastq>  --second <read_2.fastq> --check-integrity`
        
        ## Install
        
        ```
        git clone https://github.com/Clinical-Genomics/crunchy
        pip install -e .
        crunchy --help
        Usage: crunchy [OPTIONS] COMMAND [ARGS]...
        
          Base command for crunchy
        
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        Options:
          --spring-binary TEXT            Path to spring binary  [default: spring]
          --samtools-binary TEXT          Path to spring binary  [default: samtools]
          -t, --threads INTEGER           Number of threads to use for spring
                                          compression  [default: 8]
          -r, --reference TEXT            Path to reference genome
          --log-level [DEBUG|INFO|WARNING]
                                          Choose what log messages to show
          --tmp-dir TEXT                  If specific temp dir should be used
          --help                          Show this message and exit.
        
        Commands:
          auto        Run whole pipeline by compressing, comparing and deleting...
          compare     Compare two files by generating checksums.
          compress    Compress genomic files
          decompress  Decompress genomic files
        ```
        
        ## Workflow
        
        Each command can be run separately. To compress all fastq pairs below a directory run `crunchy auto spring <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.spring.fastq + file_2.spring.fastq```
        
        1. **Compare checksum with previous**
        ```file_1.spring.fastq + file_1.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
