[FEATURE] map_io reader and SAM input.

include/bio/detail/add_enum_bitwise_operators.hpp

@@ -0,0 +1,151 @@
+// -----------------------------------------------------------------------------------------------------
+// Copyright (c) 2006-2021, Knut Reinert & Freie Universität Berlin
+// Copyright (c) 2016-2021, Knut Reinert & MPI für molekulare Genetik
+// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
+// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
+// -----------------------------------------------------------------------------------------------------
+
+/*!\file
+ * \brief Provides seqan3::add_enum_bitwise_operators.
+ * \author Hannes Hauswedell <hannes.hauswedell AT fu-berlin.de>
+ */
+
+#pragma once
+
+#include <type_traits>
+
+#include <seqan3/core/platform.hpp>
+
+namespace bio::map_io
+{
+/*!\interface seqan3::enum_bitwise_operators
+ * \brief You can expect these functions on all types that overload seqan3::add_enum_bitwise_operators.
+ */
+/*!\name Requirements for seqan3::enum_bitwise_operators
+ * \relates seqan3::enum_bitwise_operators
+ * \brief You can expect these member functions.
+ * \{
+ * \fn operator&(t lhs, t rhs)
+ * \brief Returns the binary `&` operator of lhs and rhs.
+ * \param lhs First enum.
+ * \param rhs Second enum.
+ *
+ * \returns the binary conjunction of `lhs` and `rhs`.
+ *
+ * \fn operator|(t lhs, t rhs)
+ * \brief Returns the binary `|` operator of lhs and rhs.
+ * \param lhs First enum.
+ * \param rhs Second enum.
+ *
+ * \returns the binary disjunction of `lhs` and `rhs`.
+ *
+ * \fn operator^(t lhs, t rhs)
+ * \brief Returns the binary `^` operator of lhs and rhs.
+ * \param lhs First enum.
+ * \param rhs Second enum.
+ *
+ * \returns the binary XOR operation on `lhs` and `rhs`.
+ *
+ * \fn operator~(t lhs)
+ * \brief Returns the binary `~` operator of lhs.
+ * \param lhs First enum.
+ *
+ * \returns the binary NOT operation on `lhs`.
+ *
+ * \fn operator&=(t & lhs, t rhs)
+ * \brief Returns the binary `&=` operator of lhs and rhs.
+ * \param lhs First enum.
+ * \param rhs Second enum.
+ *
+ * \returns the binary AND assigment on `lhs`.
+ *
+ * \fn operator|=(t & lhs, t rhs)
+ * \brief Returns the binary `|=` operator of lhs and rhs.
+ * \param lhs First enum.
+ * \param rhs Second enum.
+ *
+ * \returns the binary OR assignment on `lhs`.
+ *
+ * \fn operator^=(t & lhs, t rhs)
+ * \brief Returns the binary `^=` operator of lhs and rhs.
+ * \param lhs First enum.
+ * \param rhs Second enum.
+ *
+ * \returns the binary XOR assignment on `lhs`.
+ * \}
+ */
+
+//!\cond DEV
+/*!\brief Set to true for a scoped enum to have binary operators overloaded.
+ * \ingroup core
+ *
+ * \details
+ *
+ * If this type trait is specialised for an enum, the binary operators `&`, `|`, `^`, `~`, `&=`, `|=`, `^=` will be
+ * added and behave just like for ints or unscoped enums.
+ *
+ * ### Example
+ *
+ * \include test/snippet/core/add_enum_bitwise_operators.cpp
+ */
+template <typename t>
+constexpr bool add_enum_bitwise_operators = false;
+
+/*!\name Binary operators for scoped enums
+ * \brief Perform binary operations like on ints or weak enums. These overloads are available if
+ * seqan3::add_enum_bitwise_operators is defined for your type.
+ * \ingroup core
+ *
+ * \details
+ *
+ * \see seqan3::add_enum_bitwise_operators
+ * \{
+ */
+template <typename t>
+constexpr t operator&(t lhs, t rhs) noexcept requires std::is_enum_v<t> && add_enum_bitwise_operators<t>
+{
+    return static_cast<t>(static_cast<std::underlying_type_t<t>>(lhs) & static_cast<std::underlying_type_t<t>>(rhs));
+}
+
+template <typename t>
+constexpr t operator|(t lhs, t rhs) noexcept requires std::is_enum_v<t> && add_enum_bitwise_operators<t>
+{
+    return static_cast<t>(static_cast<std::underlying_type_t<t>>(lhs) | static_cast<std::underlying_type_t<t>>(rhs));
+}
+
+template <typename t>
+constexpr t operator^(t lhs, t rhs) noexcept requires std::is_enum_v<t> && add_enum_bitwise_operators<t>
+{
+    return static_cast<t>(static_cast<std::underlying_type_t<t>>(lhs) ^ static_cast<std::underlying_type_t<t>>(rhs));
+}
+
+template <typename t>
+constexpr t operator~(t lhs) noexcept requires std::is_enum_v<t> && add_enum_bitwise_operators<t>
+{
+    return static_cast<t>(~static_cast<std::underlying_type_t<t>>(lhs));
+}
+
+template <typename t>
+constexpr t & operator&=(t & lhs, t rhs) noexcept requires std::is_enum_v<t> && add_enum_bitwise_operators<t>
+{
+    lhs = lhs & rhs;
+    return lhs;
+}
+
+template <typename t>
+constexpr t & operator|=(t & lhs, t rhs) noexcept requires std::is_enum_v<t> && add_enum_bitwise_operators<t>
+{
+    lhs = lhs | rhs;
+    return lhs;
+}
+
+template <typename t>
+constexpr t & operator^=(t & lhs, t rhs) noexcept requires std::is_enum_v<t> && add_enum_bitwise_operators<t>
+{
+    lhs = lhs ^ rhs;
+    return lhs;
+}
+//!\}
+//!\endcond
+
+} // namespace bio::map_io

include/bio/format/sam.hpp

@@ -0,0 +1,52 @@
+// -----------------------------------------------------------------------------------------------------
+// Copyright (c) 2006-2021, Knut Reinert & Freie Universität Berlin
+// Copyright (c) 2016-2021, Knut Reinert & MPI für molekulare Genetik
+// Copyright (c) 2020-2021, deCODE Genetics
+// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
+// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
+// -----------------------------------------------------------------------------------------------------
+
+/*!\file
+ * brief Provides the seqan3::format_sam.
+ * \author Hannes Hauswedell <hannes.hauswedell AT decode.is>
+ */
+
+#pragma once
+
+#include <string>
+#include <vector>
+
+#include <bio/platform.hpp>
+
+namespace bio
+{
+
+/*!\brief       The sam format.
+ * \ingroup     format
+ *
+ * \details
+ *
+ * This is the sam format tag. If you want to read sam files, use bio::map_io::reader, and if you want
+ * to write sam files, use bio::map_io::writer.
+ *
+ * ### Introduction
+ *
+ * sam is the de-facto-standard for mapping storage in bionformatics. See the
+ * [article on wikipedia](todo) for a an in-depth description of the format.
+ *
+ * ### Fields
+ *
+ * todo
+ *
+ * ### Implementation notes
+ *
+ * todo
+ *
+ */
+struct sam
+{
+    //!\brief The valid file extensions for this format; note that you can modify this value.
+    static inline std::vector<std::string> file_extensions{{"sam"}};
+};
+
+} // namespace bio