Metadata-Version: 1.0
Name: pySNPCall
Version: 0.1
Summary: Python implementation of Java SNP calling pipeline (https://github.com/DSGlab/SNPCallingPipeline/)
Home-page: https://github.com/baribefe/pySNPCallingPipeline/
Author: Emmanuel Naziga
Author-email: baribefe@gmail.com
License: MIT
Description:                                         ABOUT
        ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
        Python implementation of Java SNP calling pipeline (https://github.com/DSGlab/SNPCallingPipeline).
        Usage is descriped below. For consistency the configuration file is exactly as described in the Java code.
        Descriptions of the various options in the Java code is given at https://github.com/DSGlab/SNPCallingPipeline.
        An example configuration file is included in this directory.
                                               USAGE
        +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
        usage: pySNPCallingPipeline.py [-h] -c CONF_FILE [--aln_only] [--no_aln]
                                       [--local] [--submit] [--subset SUBSET]
                                       [--def_run]
        
        Run pySNPCallingPipeline
        
        optional arguments:
          -h, --help            show this help message and exit
          -c CONF_FILE, --conf CONF_FILE
                                A configuration file is required to run
                                pySNPCallingPipeline.
          --aln_only            Alignment only, default is FALSE.
          --no_aln              Run all analysis using pre-run alignments, default is
                                FALSE.
          --local               Is this a LOCAL run or should SLURM files be created?
                                Default is True.
          --submit              If running a supercomputing cluster, should only slurm
                                files be created or should the jobs be submitted as
                                well.
          --subset SUBSET       Provide a comma seperated list of a subset of
                                "alignment, getHQSNPs, intraClonalSNPs, checkSNPs,
                                filterSNPs"
          --def_run             Default: run entire calculation locally.
        
        
Platform: UNKNOWN
