From 002803f79b77fe95e9077004011efc07daa93e7f Mon Sep 17 00:00:00 2001
From: MVCowley <51127523+MVCowley@users.noreply.github.com>
Date: Mon, 18 May 2026 14:56:54 +0100
Subject: [PATCH 1/3] feat(collapse): log median UMI count per TCR

---
 src/decombinator/collapse.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/decombinator/collapse.py b/src/decombinator/collapse.py
index d81d336..b8eaeae 100644
--- a/src/decombinator/collapse.py
+++ b/src/decombinator/collapse.py
@@ -59,6 +59,7 @@
 import time
 import typing
 from importlib import metadata
+from statistics import median
 
 import networkx as nx
 import polyleven
@@ -942,6 +943,7 @@ def collapsinate(
 
     counts["number_output_unique_dcrs"] = len(collapsed)
     counts["number_output_total_dcrs"] = sum(collapsed.values())
+    counts["median_barcodes_per_tcr"] = median(collapsed.values())
 
     t1 = time.time()
     print("  ", round(t1 - t0, 2), "seconds")
@@ -1174,6 +1176,8 @@ def collapsinator(inputargs: dict, data: list = None) -> list:
             + str(counts["multi_tcr_barcodes"])
             + "\nMultiTCRBarcodeReads,"
             + str(counts["multi_tcr_barcode_reads"])
+            + "\nMedianUMIsPerTCR,"
+            + str(counts["median_barcodes_per_tcr"])
         )
 
         print(summstr, file=summaryfile)

From cb537728323d1dd0c5e5b251032c4bb86e933d99 Mon Sep 17 00:00:00 2001
From: MVCowley <51127523+MVCowley@users.noreply.github.com>
Date: Mon, 18 May 2026 15:04:41 +0100
Subject: [PATCH 2/3] feat(collapse): type standardise median stat

---
 src/decombinator/collapse.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/decombinator/collapse.py b/src/decombinator/collapse.py
index b8eaeae..b7b50e2 100644
--- a/src/decombinator/collapse.py
+++ b/src/decombinator/collapse.py
@@ -943,7 +943,7 @@ def collapsinate(
 
     counts["number_output_unique_dcrs"] = len(collapsed)
     counts["number_output_total_dcrs"] = sum(collapsed.values())
-    counts["median_barcodes_per_tcr"] = median(collapsed.values())
+    counts["median_barcodes_per_tcr"] = float(median(collapsed.values()))
 
     t1 = time.time()
     print("  ", round(t1 - t0, 2), "seconds")

From 02c8e30a9be548a625bca25f3c3b15bab0337b7c Mon Sep 17 00:00:00 2001
From: MVCowley <51127523+MVCowley@users.noreply.github.com>
Date: Mon, 18 May 2026 15:22:18 +0100
Subject: [PATCH 3/3] feat(collapse): update logging field names

---
 src/decombinator/collapse.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/decombinator/collapse.py b/src/decombinator/collapse.py
index b7b50e2..fa684cb 100644
--- a/src/decombinator/collapse.py
+++ b/src/decombinator/collapse.py
@@ -1172,9 +1172,9 @@ def collapsinator(inputargs: dict, data: list = None) -> list:
             + str(counts["readdata_fail_no_bclocs"])
             + "\nBarcodeFail_LowQuality,"
             + str(counts["readdata_fail_low_barcode_quality"])
-            + "\nMultiTCRBarcodes,"
+            + "\nNumberMultiTCRBarcodes,"
             + str(counts["multi_tcr_barcodes"])
-            + "\nMultiTCRBarcodeReads,"
+            + "\nNumberMultiTCRBarcodeReads,"
             + str(counts["multi_tcr_barcode_reads"])
             + "\nMedianUMIsPerTCR,"
             + str(counts["median_barcodes_per_tcr"])