Metadata-Version: 2.1
Name: bamAlignCleaner
Version: 0.2.1
Summary: Removes unaligned references in BAM alignment file
Home-page: https://github.com/maxibor/bamAlignCleaner
License: MIT
Description: [![bamAlignCleaner-CI](https://github.com/maxibor/bamAlignCleaner/actions/workflows/ci.yml/badge.svg)](https://github.com/maxibor/bamAlignCleaner/actions/workflows/ci.yml) [![PyPI](https://img.shields.io/pypi/v/bamAlignCleaner?color=green&label=Install%20with%20pip)](https://pypi.org/project/bamAlignCleaner/) [![Anaconda-Server Badge](https://anaconda.org/maxibor/bamaligncleaner/badges/installer/conda.svg)](https://anaconda.org/maxibor/bamaligncleaner)
        
        # bamAlignCleaner
        
        A simple utility tool to remove references with no aligned reads in a `bam`/`cram` file
        
        ## Installation
        
        * with pip 
        
        ```bash
        pip install bamAlignCleaner 
        ```
        
        * with conda
        
        ```bash
        conda install -c bioconda -c conda-forge -c maxibor bamAlignCleaner
        ```
        
        ## Usage
        
        * Quick start
        
        ```bash
        bamAlignCleaner input.bam
        ```
        
        * Advanced
        
        ```bash
        bamAlignCleaner --output output.bam --method parse input.bam
        ```
        
        ## Help
        
        ```bash
        $ bamAlignCleaner --help
        Usage: bamAlignCleaner [OPTIONS] BAM
        
          bamAlignCleaner: removes unaligned references in BAM/CRAM alignment files
          * Homepage: https://github.com/maxibor/bamAlignCleaner
          * Author: Maxime Borry
        
          BAM: BAM alignment file (sorted, and optionally indexed)
        
        Options:
          --version                       Show the version and exit.
          -m, --method [parse|index_stat]
                                          unaligned reference removal method
                                          [default: parse]
          -o, --output FILE               filtered bam file [default: STDOUT]
          --help                          Show this message and exit.
        ```
        
        ## Methods
        
        bamAlignCleaner uses either one of the two following methods to remove references not having reads mapped against them.
        
        * The `parse` method goes through each read of the alignment file and keeps the references if the read maps to it. *This method should be faster if you have more references than reads.*
        * The `check_index` checks index for the number of mapped reads to each reference. *This method should be faster if you have more reads than references.*
        
Platform: UNKNOWN
Requires-Python: >=3.6
Description-Content-Type: text/markdown
