From c866945182ed8a6d3eed422827a2decd9331fa2a Mon Sep 17 00:00:00 2001 From: Daniel Le Jeune Date: Mon, 13 Jul 2026 15:56:22 +0200 Subject: [PATCH 1/4] updates hts-sys to latest version --- .gitignore | 2 ++ Cargo.toml | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index e3a43dca2..8df839b18 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,5 @@ Cargo.lock htslib/* test/out.bam test/test_index_build.bam.csi +*.csi +*.tbx \ No newline at end of file diff --git a/Cargo.toml b/Cargo.toml index 4f0451201..e0ba8e7c0 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -21,7 +21,7 @@ bio-types = ">=0.9" byteorder = "1.3" custom_derive = "0.1" derive-new = "0.7" -hts-sys = {version = "2.2.0", default-features = false, features = ["bindgen"]} +hts-sys = {version = "2.2.1", default-features = false, features = ["bindgen"]} ieee754 = "0.2" lazy_static = "1.4" libc = "0.2" From c8af66de14f7e93f027c21f60abd0f4f4d980699 Mon Sep 17 00:00:00 2001 From: Daniel Le Jeune Date: Mon, 13 Jul 2026 16:04:30 +0200 Subject: [PATCH 2/4] more specific exclusions in the gitignore --- .gitignore | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index 8df839b18..de7f7a66a 100644 --- a/.gitignore +++ b/.gitignore @@ -6,5 +6,5 @@ Cargo.lock htslib/* test/out.bam test/test_index_build.bam.csi -*.csi -*.tbx \ No newline at end of file +built_test.csi +built_test_vcf.tbx \ No newline at end of file From c81faa9191aaf04810771f8c2fe6b796c8f99548 Mon Sep 17 00:00:00 2001 From: Daniel Le Jeune Date: Mon, 13 Jul 2026 16:13:51 +0200 Subject: [PATCH 3/4] addressing the clippy failure --- src/bam/ext.rs | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/bam/ext.rs b/src/bam/ext.rs index c02ce1b5b..8a77abcf0 100644 --- a/src/bam/ext.rs +++ b/src/bam/ext.rs @@ -452,11 +452,10 @@ impl BamRecordExtensions for bam::Record { | Cigar::Diff(len) => { result += len; } - Cigar::HardClip(len) => { - if include_hard_clip { + Cigar::HardClip(len) + if include_hard_clip => { result += len; } - } _ => {} } } From b48b9adea860e7d5175c30a9eacbd6d3fa8356cb Mon Sep 17 00:00:00 2001 From: Daniel Le Jeune Date: Mon, 13 Jul 2026 16:15:15 +0200 Subject: [PATCH 4/4] forgot to run cargo fmt --- src/bam/ext.rs | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/src/bam/ext.rs b/src/bam/ext.rs index 8a77abcf0..e4d39d1a2 100644 --- a/src/bam/ext.rs +++ b/src/bam/ext.rs @@ -452,10 +452,9 @@ 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; + } _ => {} } }