Metadata-Version: 2.1
Name: windel
Version: 0.0.1
Summary: Sliding-window indel correction
Home-page: https://github.com/J-Wall/windel
Author: Jesse Wallace
Author-email: jesse.wallace@anu.edu.au
License: UNKNOWN
Description: Windel
        ------
        
        Sliding-window INDEL correction
        
        ```
        NAME
            windel.py - Performs windowed indel analysis in a multiprocessing fashion.
        
        SYNOPSIS
            windel.py REFERENCEFILE ALIGNMENTFILE OUTFILE <flags>
        
        DESCRIPTION
            Performs windowed indel analysis in a multiprocessing fashion.
        
        POSITIONAL ARGUMENTS
            REFERENCEFILE
                path to reference fasta file
            ALIGNMENTFILE
                path to alignment file (bam/sam)
            OUTFILE
                path to output file (csv)
        
        FLAGS
            --fasta_out=FASTA_OUT
                Optional path to corrected fasta output (default None).
            --prop_thresh=PROP_THRESH
                threshold for the proportion of windowed reads having an indel at a position for an edit to be made (default 0.9)
            --window=WINDOW
                width of window to use, must be odd (default 11)
            --processes=PROCESSES
                number of processes to spawn (default is the number of cpus)
        
        NOTES
            You can also use flags syntax for POSITIONAL ARGUMENTS
        ```
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown
