Explain adapter_cutoff

Edinburgh-Genome-Foundry · Nov 25, 2024 · 943c0c1 · 943c0c1
1 parent cb960d3
commit 943c0c1
Showing 1 changed file with 4 additions and 2 deletions.
diff --git 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)