From 577ff114ea4f5c2eb24da4554a8155cbd9f3c4ec Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 15 Aug 2026 10:22:22 +0000
Subject: [PATCH 1/3] Initial plan


From 615d52a30ad3f058a71e1726a19628f46257b99b Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 15 Aug 2026 10:28:21 +0000
Subject: [PATCH 2/3] fix: satisfy clippy collapsible_match in
 seq_len_from_cigar

Co-authored-by: johanneskoester <1858646+johanneskoester@users.noreply.github.com>
---
 src/bam/ext.rs | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/bam/ext.rs b/src/bam/ext.rs
index c02ce1b5b..e4d39d1a2 100644
--- a/src/bam/ext.rs
+++ b/src/bam/ext.rs
@@ -452,10 +452,8 @@ impl BamRecordExtensions for bam::Record {
                 | Cigar::Diff(len) => {
                     result += len;
                 }
-                Cigar::HardClip(len) => {
-                    if include_hard_clip {
-                        result += len;
-                    }
+                Cigar::HardClip(len) if include_hard_clip => {
+                    result += len;
                 }
                 _ => {}
             }

From 2c5c9d1ec2dd181abd31a4825cb31cb8a4ec8773 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 15 Aug 2026 11:31:35 +0000
Subject: [PATCH 3/3] test: add hard-clip-only seq_len case

Co-authored-by: johanneskoester <1858646+johanneskoester@users.noreply.github.com>
---
 src/bam/ext.rs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/bam/ext.rs b/src/bam/ext.rs
index e4d39d1a2..eaac30e0b 100644
--- a/src/bam/ext.rs
+++ b/src/bam/ext.rs
@@ -9646,6 +9646,7 @@ mod tests {
             ("40X", 40, 40),
             ("20M5I20M", 45, 45),
             ("20M5D20M", 40, 40),
+            ("5H", 0, 5),
             ("5H35M", 35, 40),
             ("5S35M", 40, 40),
             ("35M5H", 35, 40),