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
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
Requires-Dist: fire (==0.2)
Requires-Dist: numpy (==1.17)
Requires-Dist: pysam (==0.15)
Requires-Dist: scipy (==1.4)

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
```


