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# Source code for samsifter.tools.filter_read_pmds

    # -*- coding: utf-8 -*-
    """Wrapper for PMDtools ancient read filter functionality.

    .. moduleauthor:: Florian Aldehoff <faldehoff@student.uni-tuebingen.de>
    """

    """ custom libraries """
    from samsifter.models.filter import FilterItem
    from samsifter.models.parameter import (FilterParameter, FilterThreshold)

    """ global variables """
    TEXT = "[PMDtools] Filter reads by PMDS"
    DESC = "Filtering reads by their post-mortem degradation score."

    def item():
        """Create item representing this tool in list and tree views.

        Returns
        -------
        FilterItem
            Item for use in item-based list and tree views.
        """
        item = FilterItem(text=TEXT, desc=DESC)
        item.set_command('pmdtools_mod --writesamfield --header')

        item.add_parameter(FilterThreshold(
            text="min. PMDS",
            desc="minimum post-mortem degradation score (PMDS)",
            cli_name="--threshold",
            default=3,
            minimum=-10,
            maximum=10,
            precision=0,
            required=True,
            active=True
        ))

        item.add_parameter(FilterParameter(
            text="verbose",
            desc="print additional information to STDERR",
            cli_name="--verbose",
            default=True,
            active=True
        ))

        item.add_parameter(FilterParameter(
            text="statistics",
            desc="output summarizing statistics to STDERR",
            cli_name="--stats",
            default=False
        ))

        return item

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