From 26fd4c4dcd0f74e480d20e6ecb2fbdfbcc4dd97c Mon Sep 17 00:00:00 2001
From: "seqan-actions[bot]" <seqan-actions@users.noreply.github.com>
Date: Mon, 24 Oct 2022 09:25:37 +0200
Subject: [PATCH] [MISC] clang-format

---
 include/seqan3/io/sam_file/format_bam.hpp     |  2 +-
 include/seqan3/io/sam_file/input.hpp          |  3 ++-
 include/seqan3/io/sam_file/output.hpp         |  3 ++-
 test/unit/io/sam_file/format_bam_test.cpp     |  5 +----
 test/unit/io/sam_file/sam_file_input_test.cpp | 20 +++++++++----------
 .../unit/io/sam_file/sam_file_output_test.cpp |  3 +--
 6 files changed, 16 insertions(+), 20 deletions(-)

diff --git a/include/seqan3/io/sam_file/format_bam.hpp b/include/seqan3/io/sam_file/format_bam.hpp
index bd7917006db..d5ca1362653 100644
--- a/include/seqan3/io/sam_file/format_bam.hpp
+++ b/include/seqan3/io/sam_file/format_bam.hpp
@@ -288,7 +288,7 @@ format_bam::read_alignment_record(stream_type & stream,
 
     auto stream_view = seqan3::detail::istreambuf(stream);
 
-    [[maybe_unused]] int32_t offset_tmp{}; // needed in case the cigar string was stored in the tag dictionary
+    [[maybe_unused]] int32_t offset_tmp{};  // needed in case the cigar string was stored in the tag dictionary
     [[maybe_unused]] int32_t ref_length{0}; // needed in case the cigar string was stored in the tag dictionary
 
     // Header
diff --git a/include/seqan3/io/sam_file/input.hpp b/include/seqan3/io/sam_file/input.hpp
index 66f63ce813c..3b231b9bbb2 100644
--- a/include/seqan3/io/sam_file/input.hpp
+++ b/include/seqan3/io/sam_file/input.hpp
@@ -373,7 +373,8 @@ class sam_file_input
                   "seqan3::alignment_from_cigar on how to get an alignment from the cigar information.");
 
     static_assert(
-        []() constexpr {
+        []() constexpr
+        {
             for (field f : selected_field_ids::as_array)
                 if (!field_ids::contains(f))
                     return false;
diff --git a/include/seqan3/io/sam_file/output.hpp b/include/seqan3/io/sam_file/output.hpp
index dc986e4e1bd..ec3e7020703 100644
--- a/include/seqan3/io/sam_file/output.hpp
+++ b/include/seqan3/io/sam_file/output.hpp
@@ -101,7 +101,8 @@ class sam_file_output
                              field::header_ptr>;
 
     static_assert(
-        []() constexpr {
+        []() constexpr
+        {
             for (field f : selected_field_ids::as_array)
                 if (!field_ids::contains(f))
                     return false;
diff --git a/test/unit/io/sam_file/format_bam_test.cpp b/test/unit/io/sam_file/format_bam_test.cpp
index bd3002b6521..272f4a9deec 100644
--- a/test/unit/io/sam_file/format_bam_test.cpp
+++ b/test/unit/io/sam_file/format_bam_test.cpp
@@ -590,7 +590,6 @@ TEST_F(bam_format, too_long_cigar_string_write)
     }
     too_long_cigar.push_back({1, 'M'_cigar_operation});
 
-
     // Expected output. ATTENTION this could not be validated by samtools as it does not support too long cigar strings
     std::string expected =
         std::string /*the beginning*/
@@ -658,9 +657,7 @@ TEST_F(bam_format, issue2417)
 
     std::istringstream stream{input};
 
-    seqan3::sam_file_input fin{stream,
-                               seqan3::format_bam{},
-                               seqan3::fields<seqan3::field::id, seqan3::field::cigar>{}};
+    seqan3::sam_file_input fin{stream, seqan3::format_bam{}, seqan3::fields<seqan3::field::id, seqan3::field::cigar>{}};
 
     std::vector<seqan3::gapped<seqan3::dna5>> const empty_sequence{};
 
diff --git a/test/unit/io/sam_file/sam_file_input_test.cpp b/test/unit/io/sam_file/sam_file_input_test.cpp
index c1d97b3359a..eddbbd7f0c9 100644
--- a/test/unit/io/sam_file/sam_file_input_test.cpp
+++ b/test/unit/io/sam_file/sam_file_input_test.cpp
@@ -536,11 +536,10 @@ TEST_F(sam_file_input_bam_format_f, construct_by_filename)
         filecreator << binary_input;
     }
 
-    seqan3::sam_file_input fin{
-        filename,
-        ref_ids,
-        ref_seqs,
-        seqan3::fields<seqan3::field::id, seqan3::field::seq, seqan3::field::qual>{}};
+    seqan3::sam_file_input fin{filename,
+                               ref_ids,
+                               ref_seqs,
+                               seqan3::fields<seqan3::field::id, seqan3::field::seq, seqan3::field::qual>{}};
 
     EXPECT_EQ(fin.header().ref_ids(), ref_ids);
     EXPECT_EQ(fin.header().comments[0], std::string{"This is a comment."});
@@ -562,12 +561,11 @@ TEST_F(sam_file_input_bam_format_f, construct_by_stream)
 {
     std::istringstream stream{binary_input};
 
-    seqan3::sam_file_input fin{
-        stream,
-        ref_ids,
-        ref_seqs,
-        seqan3::format_bam{},
-        seqan3::fields<seqan3::field::id, seqan3::field::seq, seqan3::field::qual>{}};
+    seqan3::sam_file_input fin{stream,
+                               ref_ids,
+                               ref_seqs,
+                               seqan3::format_bam{},
+                               seqan3::fields<seqan3::field::id, seqan3::field::seq, seqan3::field::qual>{}};
 
     EXPECT_EQ(fin.header().ref_ids(), ref_ids);
     EXPECT_EQ(fin.header().comments[0], std::string{"This is a comment."});
diff --git a/test/unit/io/sam_file/sam_file_output_test.cpp b/test/unit/io/sam_file/sam_file_output_test.cpp
index 5cc87b533a6..06c44c9a78f 100644
--- a/test/unit/io/sam_file/sam_file_output_test.cpp
+++ b/test/unit/io/sam_file/sam_file_output_test.cpp
@@ -144,8 +144,7 @@ TEST(general, default_template_args_and_deduction_guides)
         seqan3::sam_file_output fout{filename, seqan3::fields<seqan3::field::cigar>{}};
 
         using t = decltype(fout);
-        EXPECT_TRUE(
-            (std::is_same_v<typename t::selected_field_ids, seqan3::fields<seqan3::field::cigar>>)); // changed
+        EXPECT_TRUE((std::is_same_v<typename t::selected_field_ids, seqan3::fields<seqan3::field::cigar>>)); // changed
         EXPECT_TRUE((std::is_same_v<typename t::valid_formats, comp2>));
         EXPECT_TRUE((std::is_same_v<typename t::stream_char_type, comp3>));
     }