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# Source code for samsifter.tools.filter_read_identity

    # -*- coding: utf-8 -*-
    """Wrapper for PMDtools identity 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 % identity"
    DESC = ("Filtering reads with insufficient identity to their respective "
            "reference. Identity calculated according to PMDtools, activating all "
            "options will calculate identity according to MALT")

    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 --dry --writesamfield --header')

        item.add_parameter(FilterThreshold(
            text="min. identity",
            desc="minimum identity of read to reference",
            cli_name="--perc_identity",
            default=0.95,
            maximum=1.00,
            required=True,
            active=True
        ))

        item.add_parameter(FilterParameter(
            text="include indels",
            desc="treat insertions and deletions as mismatches",
            cli_name="--include_deamination",
            default=False
        ))

        item.add_parameter(FilterParameter(
            text="include deamination",
            desc="treat possibly deaminated T>C and A>G pairs as mismatches",
            cli_name="--include_deamination",
            default=False
        ))

        item.add_parameter(FilterParameter(
            text="include unknown",
            desc="treat Ns in either read or reference as mismatch",
            cli_name="--include_unknown",
            default=False
        ))

        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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