Allow manual tuning of smoothing window fraction

cnvlib/commands.py

@@ -946,6 +946,7 @@ def _cmd_fix(args):
         args.do_edge,
         args.do_rmask,
         args.cluster,
+        args.smoothing_window_fraction,
     )
     tabio.write(target_table, args.output or tgt_raw.sample_id + ".cnr")
 
@@ -992,6 +993,15 @@ def _cmd_fix(args):
 )
 P_fix.add_argument("-o", "--output", metavar="FILENAME", help="Output file name.")
 add_diploid_parx_genome(P_fix)
+P_fix.add_argument(
+    "--smoothing-window-fraction",
+    type=float,
+    help=(
+        "If specified, sets the smoothing window fraction for rolling median bias smoothing"
+        " based on traits. Otherwise, defaults to 1/sqrt(len(data))."
+    ),
+    default=None
+)
 P_fix.set_defaults(func=_cmd_fix)
 
 

cnvlib/fix.py

@@ -16,16 +16,31 @@ def do_fix(
     do_edge=True,
     do_rmask=True,
     do_cluster=False,
+    smoothing_window_fraction=None,
 ):
     """Combine target and antitarget coverages and correct for biases."""
     # Load, recenter and GC-correct target & antitarget probes separately
     logging.info("Processing target: %s", target_raw.sample_id)
     cnarr, ref_matched = load_adjust_coverages(
-        target_raw, reference, True, do_gc, do_edge, False, diploid_parx_genome
+        target_raw,
+        reference,
+        True,
+        do_gc,
+        do_edge,
+        False,
+        diploid_parx_genome,
+        smoothing_window_fraction=smoothing_window_fraction,
     )
     logging.info("Processing antitarget: %s", antitarget_raw.sample_id)
     anti_cnarr, ref_anti = load_adjust_coverages(
-        antitarget_raw, reference, False, do_gc, False, do_rmask, diploid_parx_genome
+        antitarget_raw,
+        reference,
+        False,
+        do_gc,
+        False,
+        do_rmask,
+        diploid_parx_genome,
+        smoothing_window_fraction=smoothing_window_fraction,
     )
     if len(anti_cnarr):
         # Combine target and antitarget bins
@@ -71,7 +86,16 @@ def do_fix(
     return cnarr
 
 
-def load_adjust_coverages(cnarr, ref_cnarr, skip_low, fix_gc, fix_edge, fix_rmask, diploid_parx_genome):
+def load_adjust_coverages(
+    cnarr,
+    ref_cnarr,
+    skip_low,
+    fix_gc,
+    fix_edge,
+    fix_rmask,
+    diploid_parx_genome,
+    smoothing_window_fraction=None
+):
     """Load and filter probe coverages; correct using reference and GC."""
     if "gc" in cnarr:
         # Don't choke on Picard-derived files that have the GC column
@@ -101,7 +125,9 @@ def load_adjust_coverages(cnarr, ref_cnarr, skip_low, fix_gc, fix_edge, fix_rmas
         )
     else:
         # Smoothing window fraction converges on percentile binning, like Picard
-        frac = max(0.01, len(cnarr) ** -0.5)
+        frac = smoothing_window_fraction
+        if frac is None:
+            frac = max(0.01, len(cnarr) ** -0.5)
         cnarr_index_reset = False
         if fix_gc:
             if "gc" in ref_matched: