def __init__(self, config, prefix, node, log_file=None):
input_file, has_index = self._get_input_file(node)
subnodes, dependencies = [node], node.dependencies
if not has_index:
node = BAMIndexNode(infile=input_file,
dependencies=node)
subnodes.append(node)
validation_params = ValidateBAMNode.customize(config=config,
input_bam=input_file,
output_log=log_file,
dependencies=node)
# Check MD tags against reference sequence
# FIXME: Disabled due to issues with Picard/Samtools disagreeing,
# backwards compatibility. See the discussion at
# http://sourceforge.net/mailarchive/message.php?msg_id=31348639
# validation_params.command.set_kwargs(IN_REF=prefix["Reference"])
# validation_params.command.add_option("R", "%(IN_REF)s", sep="=")
# Ignored since we may filter out misses and low-quality hits during
# mapping, which leads to a large proportion of missing PE mates.
validation_params.command.add_option("IGNORE", "MATE_NOT_FOUND",
sep="=")
# Ignored due to high rate of false positives for lanes with few hits,
# where high-quality reads may cause mis-identification of qualities
validation_params.command.add_option("IGNORE",
"INVALID_QUALITY_FORMAT", sep="=")
subnodes.append(validation_params.build_node())
description = "<w/Validation: " + str(subnodes[0])[1:]
MetaNode.__init__(self,
description=description,
subnodes=subnodes,
dependencies=dependencies)
def __init__(self, config, prefix, node, log_file=None):
input_file, has_index = self._get_input_file(node)
subnodes, dependencies = [node], node.dependencies
if not has_index:
node = BAMIndexNode(infile=input_file, dependencies=node)
subnodes.append(node)
validation_params = ValidateBAMNode.customize(config=config,
input_bam=input_file,
output_log=log_file,
dependencies=node)
# Check MD tags against reference sequence
# FIXME: Disabled due to issues with Picard/Samtools disagreeing, backwards compatibility.
# validation_params.command.set_kwargs(IN_REFERENCE = prefix["Reference"])
# validation_params.command.add_option("R", "%(IN_REFERENCE)s", sep = "=")
# Ignored since we filter out misses and low-quality hits during mapping, which
# leads to a large proportion of missing mates for PE reads.
validation_params.command.add_option("IGNORE",
"MATE_NOT_FOUND",
sep="=")
# Ignored due to high rate of false positives for lanes with few hits, where
# high-quality reads may case ValidateSamFile to mis-identify the qualities
validation_params.command.add_option("IGNORE",
"INVALID_QUALITY_FORMAT",
sep="=")
subnodes.append(validation_params.build_node())
description = "<w/Validation: " + str(subnodes[0])[1:]
MetaNode.__init__(self,
description=description,
subnodes=subnodes,
dependencies=dependencies)
def index_and_validate_bam(config, prefix, node, log_file=None):
input_file, has_index = _get_input_file(node)
if not has_index:
node = BAMIndexNode(infile=input_file, dependencies=node)
validation_params = ValidateBAMNode.customize(config=config,
input_bam=input_file,
output_log=log_file,
dependencies=node)
# Check MD tags against reference sequence
# FIXME: Disabled due to issues with Picard/Samtools disagreeing,
# backwards compatibility. See the discussion at
# http://sourceforge.net/mailarchive/message.php?msg_id=31348639
# validation_params.command.set_kwargs(IN_REF=prefix["Reference"])
# validation_params.command.add_option("R", "%(IN_REF)s", sep="=")
# Ignored since we may filter out misses and low-quality hits during
# mapping, which leads to a large proportion of missing PE mates.
validation_params.command.add_option("IGNORE", "MATE_NOT_FOUND", sep="=")
# Ignored due to high rate of false positives for lanes with few hits,
# where high-quality reads may cause mis-identification of qualities
validation_params.command.add_option("IGNORE",
"INVALID_QUALITY_FORMAT",
sep="=")
node = validation_params.build_node()
return node
def _test_validate_bams(config):
node_params = {"config" : config,
"input_bam" : "tests/data/alignments/library_1.bam",
"dependencies" : config.dependencies}
standard = ValidateBAMNode(output_log = os.path.join(config.destination, "validate_standard", "log.txt"),
**node_params)
custom = ValidateBAMNode.customize(output_log = os.path.join(config.destination, "validate_custom", "log.txt"),
**node_params)
custom.command.set_option("IGNORE_WARNINGS", "True", sep = "=")
return MetaNode(description = "ValidateSamFile",
dependencies = [standard, custom.build_node()])