diff --git a/include/bio/map_io/reader.hpp b/include/bio/map_io/reader.hpp index e5ced11..f9660af 100644 --- a/include/bio/map_io/reader.hpp +++ b/include/bio/map_io/reader.hpp @@ -8,7 +8,7 @@ /*!\file * \brief Provides bio::map_io::reader. - * \author Hannes Hauswedell + * \author Svenja Mehringer */ #pragma once @@ -16,8 +16,7 @@ #include #include -// #include -// #include +#include #include #include @@ -28,13 +27,15 @@ namespace bio::map_io // reader // ---------------------------------------------------------------------------- -/*!\brief A class for reading sam files, namely SAM, BAM. +/*!\brief A class for reading sam files, SAM, BAM. * \tparam options_t A specialisation of bio::map_io::reader_options. * \ingroup map_io * * \details * * TODO + * + * For more advanced options, see bio::map_io::reader_options. */ template class reader : public reader_base> @@ -73,10 +74,10 @@ class reader : public reader_base> // clang-format off //!\copydoc bio::reader_base::reader_base(std::istream & str, format_type const & fmt, options_t const & opt = options_t{}) // clang-format on - reader(std::istream & stream, + reader(std::istream & str, format_type const & fmt, reader_options const & opt = reader_options{}) : - base_t{stream, fmt, opt} + base_t{str, fmt, opt} {} //!\overload @@ -84,10 +85,10 @@ class reader : public reader_base> //!\cond REQ requires(!std::is_lvalue_reference_v) //!\endcond - reader(temporary_stream_t && stream, + reader(temporary_stream_t && str, format_type const & fmt, reader_options const & opt = reader_options{}) : - base_t{std::move(stream), fmt, opt} + base_t{std::move(str), fmt, opt} {} //!\brief Access the header. diff --git a/test/unit/format/sam_file_format_test_template.hpp b/test/unit/format/sam_file_format_test_template.hpp index 42d8359..564127e 100644 --- a/test/unit/format/sam_file_format_test_template.hpp +++ b/test/unit/format/sam_file_format_test_template.hpp @@ -299,7 +299,6 @@ TYPED_TEST_P(sam_file_read, warning_rnext_not_in_header) // EXPECT_THROW((fin.begin()), seqan3::format_error); // } - // // ---------------------------------------------------------------------------- // // sam_file_write // // ----------------------------------------------------------------------------