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nodes.py
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nodes.py
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#!/usr/bin/python3
#
# Copyright (c) 2012 Mikkel Schubert <MikkelSch@gmail.com>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
#
from paleomix.nodes.picard import ValidateBAMNode
from paleomix.nodes.samtools import BAMIndexNode
def index_and_validate_bam(config, prefix, node, log_file=None, create_index=True):
input_file, index_file = _get_input_files(node, prefix["IndexFormat"])
if not index_file and create_index:
node = BAMIndexNode(
infile=input_file, index_format=prefix["IndexFormat"], dependencies=node
)
(index_file,) = node.output_files
ignored_checks = [
# Ignored since we may filter out misses and low-quality hits during
# mapping, which leads to a large proportion of missing PE mates.
"MATE_NOT_FOUND",
# Ignored due to high rate of false positives for lanes with few hits,
# where high-quality reads may cause mis-identification of qualities
"INVALID_QUALITY_FORMAT",
]
return ValidateBAMNode(
config=config,
input_bam=input_file,
input_index=index_file,
ignored_checks=ignored_checks,
big_genome_mode=prefix["IndexFormat"] == ".csi",
output_log=log_file,
dependencies=node,
)
def _get_input_files(node, index_format):
index_filename = None
input_filename = None
for filename in node.output_files:
if filename.lower().endswith(index_format):
index_filename = True
elif filename.lower().endswith(".bam"):
input_filename = filename
return input_filename, index_filename