def validate_umi_depth_metrics(metrics_file):
""" Validate depth related umi metrics
metrics_file : str ; path to the metrics file
"""
## Parse the values from the summary file first
metrics = utils.parse_summary_file(metrics_file)
## Check values
assert utils.compare_with_tolerance(metrics["mean UMI depth"],
MEAN_UMI_DEPTH, 0.02) is True
assert utils.compare_with_tolerance(metrics["mean read depth"],
MEAN_READ_DEPTH, 0.02) is True
def validate_umi_read_frags_metrics(metrics_file):
""" Validate metrics related to read frags and umi
metrics_file : str ; path to the metrics file
"""
## Parse the values from the summary file first
metrics = utils.parse_summary_file(metrics_file)
assert utils.compare_with_tolerance(metrics["UMIs"], UMIs, 0.02) is True
assert utils.compare_with_tolerance(metrics["read fragments per MT, mean"],
READS_PER_MT, 0.02) is True
assert utils.compare_with_tolerance(
metrics["% of reads from internal downstream priming"],
READS_FROM_INTERNAL_DOWNSTREAM_PRIMING, 0.02) is True
def validate_umi_filter_metrics(metrics_file):
""" Validate metrics related to how the reads were filtered
metrics_file : str ; path to the metrics file
"""
## Parse the values from the summary file first
metrics = utils.parse_summary_file(metrics_file)
assert utils.compare_with_tolerance(
metrics["read fragments dropped, R1 or R2 not mapped"],
READS_DROPPED_R1_R2_UNMAPPED, 0.02) is True
assert utils.compare_with_tolerance(
metrics[
"read fragments dropped, not passing mapping filters (low mapq, split alignments, discordant pairs, etc.)"],
READS_DROPPED_MAPPING_FILTERS, 0.02) is True
assert utils.compare_with_tolerance(
metrics["read fragments dropped, off target"],
READS_DROPPED_OFF_TARGET, 0.02) is True
def validate_variant_calling_metrics(metrics_file):
""" Validate metrics related
metrics_file : str ; path to the metrics file
"""
## Parse the values from the summary file first
metrics = utils.parse_summary_file(metrics_file)
assert utils.compare_with_tolerance(
metrics["variants called by smCounter"], VARIANTS_CALLED, 0) is True