From cebfe2fe0083db4c8c3b70484d2b34c23ee3e1c3 Mon Sep 17 00:00:00 2001
From: Xiaoyu Chen <xchen@illumina.com>
Date: Thu, 1 Feb 2018 15:39:28 -0800
Subject: [PATCH] Minor fixes for clang compilers

---
 src/c++/lib/applications/TestAssembler/extractAssemblyReads.hh | 1 -
 src/c++/lib/htsapi/bam_streamer.hh                             | 2 +-
 src/c++/lib/manta/test/testUtil.hh                             | 2 +-
 src/c++/lib/options/IterativeAssemblerOptions.hh               | 2 +-
 src/c++/lib/options/SVRefinerOptions.hh                        | 1 -
 src/c++/lib/options/SmallAssemblerOptions.hh                   | 2 +-
 6 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/src/c++/lib/applications/TestAssembler/extractAssemblyReads.hh b/src/c++/lib/applications/TestAssembler/extractAssemblyReads.hh
index b301b3ba..e35b858e 100644
--- a/src/c++/lib/applications/TestAssembler/extractAssemblyReads.hh
+++ b/src/c++/lib/applications/TestAssembler/extractAssemblyReads.hh
@@ -21,7 +21,6 @@
 
 #include "assembly/AssemblyReadInfo.hh"
 #include "options/ReadScannerOptions.hh"
-#include "options/SmallAssemblerOptions.hh"
 #include "options/IterativeAssemblerOptions.hh"
 
 typedef IterativeAssemblerOptions AssemblerOptions;
diff --git a/src/c++/lib/htsapi/bam_streamer.hh b/src/c++/lib/htsapi/bam_streamer.hh
index 6b26e60b..c0e01702 100644
--- a/src/c++/lib/htsapi/bam_streamer.hh
+++ b/src/c++/lib/htsapi/bam_streamer.hh
@@ -66,7 +66,7 @@ struct bam_streamer : public stream_state_reporter, public boost::noncopyable
         const char* referenceFilename,
         const char* region = nullptr);
 
-    ~bam_streamer();
+    ~bam_streamer() override;
 
     /// \brief Set new region to iterate over, this will fail if the alignment file is not indexed
     ///
diff --git a/src/c++/lib/manta/test/testUtil.hh b/src/c++/lib/manta/test/testUtil.hh
index 4a6eab1d..68437420 100644
--- a/src/c++/lib/manta/test/testUtil.hh
+++ b/src/c++/lib/manta/test/testUtil.hh
@@ -181,7 +181,7 @@ void addSupplementaryEvidence(
 {
     const char svtag[] = {'S','A'};
     bam_aux_append(bamRead.get_data(),svtag,'Z',(svStr.size()+1),
-                   (uint8_t*)(svStr.c_str()));
+                   reinterpret_cast<uint8_t*>(const_cast<char*>(svStr.c_str())));
 }
 
 /// \brief Create the BamAlignment for a given read using the SimpleAlignment object.
diff --git a/src/c++/lib/options/IterativeAssemblerOptions.hh b/src/c++/lib/options/IterativeAssemblerOptions.hh
index bc8445d9..e27ed909 100644
--- a/src/c++/lib/options/IterativeAssemblerOptions.hh
+++ b/src/c++/lib/options/IterativeAssemblerOptions.hh
@@ -24,7 +24,7 @@
 ///
 struct IterativeAssemblerOptions
 {
-    IterativeAssemblerOptions() = default;
+    IterativeAssemblerOptions() {}
 
     /// the symbol set used during assembly
     std::string alphabet = "ACGT";
diff --git a/src/c++/lib/options/SVRefinerOptions.hh b/src/c++/lib/options/SVRefinerOptions.hh
index e61f60c4..9bf8a311 100644
--- a/src/c++/lib/options/SVRefinerOptions.hh
+++ b/src/c++/lib/options/SVRefinerOptions.hh
@@ -21,7 +21,6 @@
 
 #include "alignment/AlignmentScores.hh"
 #include "options/IterativeAssemblerOptions.hh"
-#include "options/SmallAssemblerOptions.hh"
 
 typedef IterativeAssemblerOptions AssemblerOptions;
 
diff --git a/src/c++/lib/options/SmallAssemblerOptions.hh b/src/c++/lib/options/SmallAssemblerOptions.hh
index 1c3a5cb1..e4366977 100644
--- a/src/c++/lib/options/SmallAssemblerOptions.hh
+++ b/src/c++/lib/options/SmallAssemblerOptions.hh
@@ -24,7 +24,7 @@
 ///
 struct SmallAssemblerOptions
 {
-    SmallAssemblerOptions() = default;
+    SmallAssemblerOptions() {}
 
     /// the symbol set used during assembly
     std::string alphabet = "ACGT";