[FEATURE] Allow setting warning stream for sam file

include/seqan3/io/sam_file/detail/format_sam_base.hpp

@@ -21,6 +21,7 @@
 #include <seqan3/io/detail/misc.hpp>
 #include <seqan3/io/sam_file/detail/cigar.hpp>
 #include <seqan3/io/sam_file/header.hpp>
+#include <seqan3/io/sam_file/input_options.hpp>
 #include <seqan3/io/sam_file/output_format_concept.hpp>
 #include <seqan3/utility/detail/type_name_as_string.hpp>
 #include <seqan3/utility/views/repeat_n.hpp>
@@ -82,10 +83,11 @@ class format_sam_base
     template <arithmetic arithmetic_target_type>
     void read_arithmetic_field(std::string_view const & str, arithmetic_target_type & arithmetic_target);
 
-    template <typename stream_view_type, typename ref_ids_type, typename ref_seqs_type>
+    template <typename stream_view_type, typename ref_ids_type, typename ref_seqs_type, typename seq_legal_alph_type>
     void read_header(stream_view_type && stream_view,
                      sam_file_header<ref_ids_type> & hdr,
-                     ref_seqs_type & /*ref_id_to_pos_map*/);
+                     ref_seqs_type & /*ref_id_to_pos_map*/,
+                     sam_file_input_options<seq_legal_alph_type> const & options);
 
     template <typename stream_t, typename header_type>
     void write_header(stream_t & stream, sam_file_output_options const & options, header_type & header);
@@ -270,10 +272,11 @@ inline void format_sam_base::read_arithmetic_field(std::string_view const & str,
  * not in a correct state (e.g. required fields are not given), but throwing might occur downstream of the actual
  * error.
  */
-template <typename stream_view_type, typename ref_ids_type, typename ref_seqs_type>
+template <typename stream_view_type, typename ref_ids_type, typename ref_seqs_type, typename seq_legal_alph_type>
 inline void format_sam_base::read_header(stream_view_type && stream_view,
                                          sam_file_header<ref_ids_type> & hdr,
-                                         ref_seqs_type & /*ref_id_to_pos_map*/)
+                                         ref_seqs_type & /*ref_id_to_pos_map*/,
+                                         sam_file_input_options<seq_legal_alph_type> const & options)
 {
     auto it = std::ranges::begin(stream_view);
     auto end = std::ranges::end(stream_view);
@@ -335,9 +338,13 @@ inline void format_sam_base::read_header(stream_view_type && stream_view,
         read_forward_range_field(string_buffer, value);
     };
 
-    auto print_cerr_of_unspported_tag = [](char const * const header_tag, std::array<char, 2> raw_tag)
+    auto print_cerr_of_unspported_tag = [&options](char const * const header_tag, std::array<char, 2> raw_tag)
     {
-        std::cerr << "Unsupported SAM header tag in @" << header_tag << ": " << raw_tag[0] << raw_tag[1] << '\n';
+        if (options.warning_stream == nullptr)
+            return;
+
+        *options.warning_stream << "Unsupported SAM header tag in @" << header_tag << ": " << raw_tag[0] << raw_tag[1]
+                                << '\n';
     };
 
     while (it != end && is_char<'@'>(*it))

include/seqan3/io/sam_file/format_bam.hpp

@@ -262,7 +262,7 @@ template <typename stream_type, // constraints checked by file
           typename bit_score_type>
 inline void
 format_bam::read_alignment_record(stream_type & stream,
-                                  sam_file_input_options<seq_legal_alph_type> const & SEQAN3_DOXYGEN_ONLY(options),
+                                  sam_file_input_options<seq_legal_alph_type> const & options,
                                   ref_seqs_type & ref_seqs,
                                   sam_file_header<ref_ids_type> & header,
                                   stream_pos_type & position_buffer,
@@ -308,7 +308,7 @@ format_bam::read_alignment_record(stream_type & stream,
         read_integral_byte_field(stream_view, l_text);
 
         if (l_text > 0) // header text is present
-            read_header(stream_view | detail::take_exactly_or_throw(l_text), header, ref_seqs);
+            read_header(stream_view | detail::take_exactly_or_throw(l_text), header, ref_seqs, options);
 
         read_integral_byte_field(stream_view, n_ref);
 

include/seqan3/io/sam_file/format_sam.hpp

@@ -356,7 +356,7 @@ template <typename stream_type, // constraints checked by file
           typename bit_score_type>
 inline void
 format_sam::read_alignment_record(stream_type & stream,
-                                  sam_file_input_options<seq_legal_alph_type> const & SEQAN3_DOXYGEN_ONLY(options),
+                                  sam_file_input_options<seq_legal_alph_type> const & options,
                                   ref_seqs_type & ref_seqs,
                                   sam_file_header<ref_ids_type> & header,
                                   stream_pos_type & position_buffer,
@@ -389,7 +389,7 @@ format_sam::read_alignment_record(stream_type & stream,
     // -------------------------------------------------------------------------------------------------------------
     if (is_char<'@'>(*stream_it)) // we always read the header if present
     {
-        read_header(stream_view, header, ref_seqs);
+        read_header(stream_view, header, ref_seqs, options);
 
         if (std::ranges::begin(stream_view) == std::ranges::end(stream_view)) // file has no records
             return;

include/seqan3/io/sam_file/input_options.hpp

@@ -9,6 +9,8 @@
 
 #pragma once
 
+#include <iostream>
+
 #include <seqan3/core/platform.hpp>
 
 namespace seqan3
@@ -22,7 +24,7 @@ namespace seqan3
 template <typename sequence_legal_alphabet>
 struct sam_file_input_options
 {
-    // options to define
+    std::ostream * warning_stream{std::addressof(std::cerr)};
 };
 
 } // namespace seqan3