diff --git a/ediacara/Comparator.py b/ediacara/Comparator.py index 67ffc5d..d1da8fe 100644 --- a/ediacara/Comparator.py +++ b/ediacara/Comparator.py @@ -748,8 +748,10 @@ def get_unaligned_interval_sizes(self): interval = P.closed(row["query_start"], row["query_end"]) alignment_intervals = alignment_intervals | interval - # Older reads begin with a ~100 bp unaligned (adapter) segment which is - # removed in newer versions. Value is set to zero: + # Sequencing software can automatically trim adapters. + # Untrimmed reads begin with a ~100 bp unaligned (adapter) segment. + # Inserts of that size can be ignored using the parameter below. + # We expect trimmed reads, therefore the value is set to zero: adapter_cutoff = 0 read_interval = P.closed(adapter_cutoff, row["query_length"]) discretized_alignment_intervals = self.discretize(alignment_intervals)