[WIP] Ann io

include/bio/ann_io/header.hpp

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+// -----------------------------------------------------------------------------------------------------
+// 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 bio::var_io::header and various auxiliary classes.
+ * \author Hannes Hauswedell <hannes.hauswedell AT decode.is>
+ */
+
+#pragma once
+
+#include <string>
+#include <string_view>
+#include <utility>
+#include <vector>
+
+#include <bio/detail/charconv.hpp>
+#include <bio/detail/views_eager_split.hpp>
+#include <bio/exception.hpp>
+#include <bio/misc.hpp>
+#include <bio/ann_io/misc.hpp>
+
+namespace bio::ann_io
+{
+class header
+{
+public:
+    std::vector<std::pair<std::string, std::string>> browser_values{};
+    std::vector<std::pair<std::string, std::string>> track_values{};
+
+    /*!\name Constructors, destructor and assignment
+     * \{
+     */
+    //!\brief Default construction.
+    header()                           = default; //!< Defaulted.
+    header(header const &)             = default; //!< Defaulted.
+    header(header &&)                  = default; //!< Defaulted.
+    ~header()                          = default; //!< Defaulted.
+    header & operator=(header const &) = default; //!< Defaulted.
+    header & operator=(header &&)      = default; //!< Defaulted.
+
+    //!\brief Construct from a header given as plaintext.
+    explicit header(std::string_view plaintext_header)
+    {
+        if (plaintext_header.ends_with("\r\n"))
+            plaintext_header = plaintext_header.substr(0, plaintext_header.size() - 2);
+        else if (plaintext_header.ends_with("\n"))
+            plaintext_header = plaintext_header.substr(0, plaintext_header.size() - 1);
+
+        for (std::string_view const line : plaintext_header | detail::eager_split('\n'))
+            parse_line(line);
+    }
+
+    /*!\name Convert to plaintext ("raw") header
+     * \{
+     */
+    //!\brief Converts the header to plaintext (includes IDX entries).
+    std::string to_plaintext() const { return to_plaintext_impl(); }
+    //!\}
+
+private:
+    void parse_line(std::string_view const l)
+    {
+        if (l.starts_with("browser"))
+        {
+            auto pair_split = l.substr(8) | detail::eager_split(' ');
+            auto it1        = pair_split.begin();
+            auto it2        = std::ranges::next(it1);
+            auto it3        = std::ranges::next(it2); // TODO whats going on here?
+
+            if (it1 == std::default_sentinel || it2 == std::default_sentinel) //|| it3 != std::default_sentinel)
+            {
+                throw format_error{std::string{"Could not parse the following string into a dictionary: "} +
+                                   std::string{l}};
+            }
+
+            browser_values.emplace_back(static_cast<std::string>(*it1), static_cast<std::string>(*it2));
+        }
+        else if (l.starts_with("track"))
+        {
+            for (std::string_view const pair : l.substr(6) | detail::eager_split(' ', true))
+            {
+                auto pair_split = pair | detail::eager_split('=');
+                auto it1        = pair_split.begin();
+                auto it2        = std::ranges::next(it1);
+
+                if (it1 == std::default_sentinel || it2 == std::default_sentinel) //|| it3 != std::default_sentinel)
+                {
+                    throw format_error{std::string{"Could not parse the following string into a dictionary: "} +
+                                       std::string{pair}};
+                }
+
+                track_values.emplace_back(static_cast<std::string>(*it1), static_cast<std::string>(strip_quotes(*it2)));
+            }
+        }
+    }
+
+    //!\brief Return a substring from the argument that does not contain enclosing quotes (if present).
+    static inline std::string_view strip_quotes(std::string_view const in)
+    {
+        return (in.size() < 2 || in.front() != '"' || in.back() != '"') ? in : in.substr(1, in.size() - 2);
+    }
+
+    /*!\name Functions for converting to text
+     * \{
+     */
+    //!\brief Implementation function for creating the plaintext header.
+    std::string to_plaintext_impl() const
+    {
+        std::string raw_data;
+
+        constexpr auto quote_wrap = [](std::string in)
+        {
+            if (in.size() == 0)
+                in = "\"\"";
+            else if (in.front() != '\"')
+                in.insert(in.begin(), '\"');
+
+            if (in.size() == 1 || in.back() != '\"')
+                in.push_back('\"');
+
+            return in;
+        };
+
+        constexpr auto is_number = [](const std::string& s)
+        {
+            std::string::const_iterator it = s.begin();
+            while (it != s.end() && std::isdigit(*it)) ++it;
+            return !s.empty() && it == s.end();
+        };
+
+        /* First print out browser settings one per line */
+
+        for (auto const & e : browser_values)
+        {
+            (((((raw_data += "browser ") += e.first) += ' ') += e.second) += '\n');
+        }
+        /* Then print out track settings all on the same line. */
+        raw_data += "track ";
+        for (auto const & e : track_values)
+        {
+            ((((raw_data += e.first) += '=') += is_number(e.second) ? e.second : quote_wrap(e.second)) += ' ');
+        }
+
+        return raw_data.substr(0, raw_data.size() - 1) + '\n';
+    }
+    //
+    // //!\brief Turn bio::value_type_id into string.
+    // static std::string unparse_type(value_type_id const id)
+    // {
+    //     // TODO replace with string_view
+    //     switch (id)
+    //     {
+    //         case value_type_id::int8:
+    //         case value_type_id::vector_of_int8:
+    //         case value_type_id::int16:
+    //         case value_type_id::vector_of_int16:
+    //         case value_type_id::int32:
+    //         case value_type_id::vector_of_int32:
+    //             return "Integer";
+    //         case value_type_id::float32:
+    //         case value_type_id::vector_of_float32:
+    //             return "Float";
+    //         case value_type_id::char8:
+    //         case value_type_id::vector_of_char8:
+    //             return "Character";
+    //         case value_type_id::string:
+    //         case value_type_id::vector_of_string:
+    //             return "String";
+    //         case value_type_id::flag:
+    //             return "Flag";
+    //         default:
+    //             throw format_error{"Illegal type in INFO or FILTER header line."};
+    //     }
+    //     return "";
+    // }
+    //!\}
+};
+}

include/bio/ann_io/misc.hpp

@@ -0,0 +1,67 @@
+// -----------------------------------------------------------------------------------------------------
+// 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 bio::var_io::tag_dictionary class and auxiliaries.
+ * \author Joshua Kim <kim_j AT molgen.mpg.de>
+ */
+
+ #pragma once
+
+ #include <bio/misc.hpp>
+ #include <bio/record.hpp>
+
+namespace bio::ann_io
+{
+//-----------------------------------------------------------------------------
+// default_field_ids
+//-----------------------------------------------------------------------------
+
+//!\brief Default fields for bio::var_io::reader_options.
+//!\ingroup var_io
+inline constinit auto default_field_ids = vtag<field::chrom,
+                                               field::chromStart,
+                                               field::chromEnd>;
+
+//-----------------------------------------------------------------------------
+// Pre-defined field types (reader)
+//-----------------------------------------------------------------------------
+
+/*!\name Pre-defined field types
+* \brief These can be used to configure the behaviour of the bio::var_io::reader via bio::var_io::reader_options.
+* \{
+*/
+/*!\brief The default field types for variant io.
+*!\ingroup var_io
+*
+* \details
+*
+* These traits define a record type with minimal memory allocations for all input formats.
+* It is the recommended record type when iterating ("streaming") over files that ca be any variant IO format.
+*
+* The "style" of the record resembles the VCF specification, i.e. contigs, FILTERs and INFO identifiers are
+* represented as string/string_views. **However,** the genotypes are encoded by-genotype (BCF-style) and not by-sample
+* (VCF-style) for performance reasons.
+*
+* See bio::var_io::genotypes_bcf_style for more information on the latter.
+*/
+template <ownership own = ownership::shallow>
+inline constinit auto field_types =
+ttag<std::string_view,                          // field::chrom,
+     uint32_t,                                  // field::chromStart,
+     uint32_t>;                                 // field::chromEnd
+
+//!\brief Deep version of bio::var_io::field_types.
+//!\ingroup var_io
+template <>
+inline constinit auto field_types<ownership::deep> =
+ttag<std::string,                                     // field::chrom,
+     uint32_t,                                        // field::chromStart,
+     uint32_t>;                                       // field::chromEnd
+
+}

include/bio/ann_io/reader.hpp

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+// -----------------------------------------------------------------------------------------------------
+// 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 bio::ann_io::reader.
+ * \author Joshua Kim <kim_j AT molgen.mpg.de>
+ */
+
+ #pragma once
+
+ #include <filesystem>
+
+ #include <bio/detail/reader_base.hpp>
+ #include <bio/ann_io/reader_options.hpp>
+ #include <bio/ann_io/header.hpp>
+ #include <bio/format/bed_input_handler.hpp>
+
+namespace bio::ann_io
+{
+template <typename... option_args_t>
+class reader : public reader_base<reader<option_args_t...>, reader_options<option_args_t...>>
+{
+private:
+    //!\brief The base class.
+    using base_t      = reader_base<reader<option_args_t...>, reader_options<option_args_t...>>;
+    //!\brief Inherit the format_type definition.
+    using format_type = typename base_t::format_type;
+    /* Implementation note
+     * format_type is "inherited" as private here to avoid appearing twice in the documentation.
+     * Its actual visibility is public because it is public in the base class.
+     */
+    //!\brief Make the format handler visible.
+    using base_t::format_handler;
+
+    //!\brief A pointer to the header inside the format.
+    bio::ann_io::header const * header_ptr = nullptr;
+public:
+    // clang-format off
+    //!\copydoc bio::reader_base::reader_base(std::filesystem::path const & filename, format_type const & fmt, options_t const & opt = options_t{})
+    // clang-format on
+    reader(std::filesystem::path const &            filename,
+           format_type const &                      fmt,
+           reader_options<option_args_t...> const & opt = reader_options<option_args_t...>{}) :
+      base_t{filename, fmt, opt}
+    {}
+
+    //!\overload
+    explicit reader(std::filesystem::path const &            filename,
+                    reader_options<option_args_t...> const & opt = reader_options<option_args_t...>{}) :
+      base_t{filename, opt}
+    {}
+
+    // 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 &                           str,
+           format_type const &                      fmt,
+           reader_options<option_args_t...> const & opt = reader_options<option_args_t...>{}) :
+      base_t{str, fmt, opt}
+    {}
+
+    //!\overload
+    template <movable_istream temporary_stream_t>
+        //!\cond REQ
+        requires(!std::is_lvalue_reference_v<temporary_stream_t>)
+    //!\endcond
+    reader(temporary_stream_t &&                    str,
+           format_type const &                      fmt,
+           reader_options<option_args_t...> const & opt = reader_options<option_args_t...>{}) :
+      base_t{std::move(str), fmt, opt}
+    {}
+
+    //!\brief Access the header.
+    bio::ann_io::header const & header()
+    {
+        if (header_ptr == nullptr)
+        {
+            // ensure that the format_handler is created
+            this->begin();
+
+            header_ptr = std::visit([](auto const & handler) { return &handler.get_header(); }, format_handler);
+        }
+
+        return *header_ptr;
+    }
+};
+}