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# Source code for samsifter.tools.sort_by_coordinates

    # -*- coding: utf-8 -*-
    """Wrapper for SAMtools sort functionality for sorting reads by coordinates.

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

    """ custom libraries """
    from samsifter.models.filter import FilterItem

    """ global variables """
    TEXT = "[SAMtools] Sort by coordinates"
    DESC = ("Resorts entries in a BAM file by their coordinates.")

    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, icon=FilterItem.ICON_SORTER)

        # input/output is not default (SAM sorted by queryname)
        item.set_input_format('BAM')
        item.set_input_sorting('queryname')
        item.set_output_format('BAM')
        item.set_output_sorting('coordinate')

        item.set_command('samtools sort - tmp -o')
        return item

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