Source code for samsifter.tools.sam_2_bam
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Wrapper for SAMtools view functionality to convert SAM to BAM 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 SAM to BAM format"
DESC = ("Converts the text-based SAM format to the binary BAM format.")
[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_CONVERTER)
item.set_command('samtools view -S -b -')
item.add_parameter(FilterParameter(
text="uncompressed BAM output",
desc=("skip compression of the binary format to speed up following "
"SAMtools steps"),
cli_name='-u',
default=False,
required=False,
active=False
))
# input/output is not default (SAM sorted by queryname)
item.set_input_format('SAM')
item.set_input_sorting('any')
item.set_output_format('BAM')
item.set_output_sorting('as_input')
return item