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# Source code for samsifter.tools.bam_2_sam

    # -*- coding: utf-8 -*-
    """Wrapper for SAMtools view functionality converting BAM to SAM files.

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

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

    """ global variables """
    TEXT = "[SAMtools] Convert BAM to SAM format"
    DESC = ("Converts the binary BAM format to the text-based SAM format.")

    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_CONVERTER)
        item.set_command('samtools view -')

        item.add_parameter(FilterParameter(
            text="print header",
            desc="include header in output",
            cli_name='-h',
            default=True,
            active=True
        ))

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

        return item

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