Source code for samsifter.filters.sort_by_coordinates

# -*- coding: utf-8 -*-
"""
Wrapper for SAMtools sort

.. 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.")


[docs]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