[FIX] libc++: tellg invalidates I/O buffer

seqan · Nov 12, 2023 · 285f8e8 · 285f8e8
1 parent 6948b70
commit 285f8e8
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Showing 5 changed files with 20 additions and 9 deletions.
diff --git a/include/seqan3/io/sequence_file/format_embl.hpp b/include/seqan3/io/sequence_file/format_embl.hpp
@@ -105,12 +105,14 @@ class format_embl
                               id_type & id,
                               qual_type & SEQAN3_DOXYGEN_ONLY(qualities))
     {
+        // Store current position in buffer
+        // Must happen before construction the view.
+        // With libc++, tellg invalidates the I/O buffer.
+        position_buffer = stream.tellg();
+
         auto stream_view = detail::istreambuf(stream);
         auto stream_it = std::ranges::begin(stream_view);
 
-        // Store current position in buffer.
-        position_buffer = stream.tellg();
-
         std::string idbuffer;
         std::ranges::copy(stream_view | detail::take_until_or_throw(is_cntrl || is_blank),
                           std::back_inserter(idbuffer));

diff --git a/include/seqan3/io/sequence_file/format_fasta.hpp b/include/seqan3/io/sequence_file/format_fasta.hpp
@@ -117,11 +117,13 @@ class format_fasta
                               id_type & id,
                               qual_type & SEQAN3_DOXYGEN_ONLY(qualities))
     {
-        auto stream_view = detail::istreambuf(stream);
-
         // Store current position in buffer
+        // Must happen before construction the view.
+        // With libc++, tellg invalidates the I/O buffer.
         position_buffer = stream.tellg();
 
+        auto stream_view = detail::istreambuf(stream);
+
         // ID
         read_id(stream_view, options, id);
 

diff --git a/include/seqan3/io/sequence_file/format_fastq.hpp b/include/seqan3/io/sequence_file/format_fastq.hpp
@@ -109,6 +109,11 @@ class format_fastq
                               id_type & id,
                               qual_type & qualities)
     {
+        // Store current position in buffer
+        // Must happen before construction the view.
+        // With libc++, tellg invalidates the I/O buffer.
+        position_buffer = stream.tellg();
+
         auto stream_view = detail::istreambuf(stream);
         auto stream_it = std::ranges::begin(stream_view);
 
@@ -117,7 +122,6 @@ class format_fastq
         size_t sequence_size_after = 0;
         if constexpr (!detail::decays_to_ignore_v<seq_type>)
             sequence_size_before = size(sequence);
-        position_buffer = stream.tellg();
 
         /* ID */
         if (*stream_it != '@') // [[unlikely]]

diff --git a/include/seqan3/io/sequence_file/format_genbank.hpp b/include/seqan3/io/sequence_file/format_genbank.hpp
@@ -106,12 +106,14 @@ class format_genbank
                               id_type & id,
                               qual_type & SEQAN3_DOXYGEN_ONLY(qualities))
     {
+        // Store current position in buffer
+        // Must happen before construction the view.
+        // With libc++, tellg invalidates the I/O buffer.
+        position_buffer = stream.tellg();
+
         auto stream_view = detail::istreambuf(stream);
         auto stream_it = std::ranges::begin(stream_view);
 
-        // Store current position in buffer.
-        position_buffer = stream.tellg();
-
         if (!(std::ranges::equal(stream_view | detail::take_until_or_throw(is_cntrl || is_blank),
                                  std::string{"LOCUS"})))
             throw parse_error{"An entry has to start with the code word LOCUS."};

diff --git a/include/seqan3/io/stream/detail/fast_istreambuf_iterator.hpp b/include/seqan3/io/stream/detail/fast_istreambuf_iterator.hpp
@@ -229,6 +229,7 @@ class fast_istreambuf_iterator
     reference operator*() const
     {
         assert(stream_buf != nullptr);
+        assert(stream_buf->gptr() != stream_buf->egptr());
         return *stream_buf->gptr();
     }