Source code for samsifter.filters.remove_duplicates

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

.. 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] Remove duplicates"
DESC = ("Removes duplicate reads with identical start 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) item.set_command('samtools rmdup - -') item.add_parameter(FilterParameter( text="rmdup for SE reads", desc="remove duplicate single-end reads", cli_name='-s', default=True, required=False, active=True )) item.add_parameter(FilterParameter( text="treat PE as SE", desc="treat paired-end reads as single-end reads", cli_name='-S', default=False, required=False, active=False)) # input/output is not default (SAM sorted by queryname) item.set_input_format('BAM') item.set_input_sorting('coordinate') item.set_output_format('BAM') item.set_output_sorting('coordinate') return item