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[FIX] Accept user-defined tags
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@eseiler
eseiler committed Jun 3, 2024
1 parent da6a491 commit 72f288d
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Showing 5 changed files with 99 additions and 76 deletions.
33 changes: 14 additions & 19 deletions include/seqan3/io/sam_file/detail/format_sam_base.hpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -269,8 +269,11 @@ inline void format_sam_base::read_arithmetic_field(std::string_view const & str,
* The function throws a seqan3::format_error if the format is not in a correct state (e.g. required fields are not
* given), but throwing might occur downstream of the actual error.
*
* If any unknown tag was encountered, a warning will be emitted to std::cerr. This can be configured with
* seqan3::sam_file_input_options::stream_warnings_to.
* Any user-defined tags are not checked for correctness ([TAG]:[VALUE]) and are stored as strings:
* * HD: seqan3::sam_file_header::user_tags
* * SQ: seqan3::sam_file_header::ref_id_info
* * RG: seqan3::sam_file_header::read_groups
* * PG: seqan3::sam_file_header::program_infos / seqan3::sam_file_program_info_t::user_tags
*/
template <typename stream_view_type, typename ref_ids_type, typename ref_seqs_type>
inline void format_sam_base::read_header(stream_view_type && stream_view,
Expand Down Expand Up @@ -337,20 +340,6 @@ inline void format_sam_base::read_header(stream_view_type && stream_view,
read_forward_range_field(string_buffer, value);
};

auto consume_unsupported_tag_and_print_warning =
[&](char const * const header_tag, std::array<char, 2> const raw_tag)
{
// Not using `copy_next_tag_value_into_buffer` because we do not care whether the tag is valid.
// E.g., `pb5.0.0` instead of `pb:5.0.0`, would break the parsing if we used `copy_next_tag_value_into_buffer`.
take_until_predicate(is_char<'\t'> || is_char<'\n'>);

if (options.stream_warnings_to == nullptr)
return;

*options.stream_warnings_to << "Unsupported tag found in SAM header @" << header_tag << ": \"" << raw_tag[0]
<< raw_tag[1] << string_buffer << "\"\n";
};

while (it != end && is_char<'@'>(*it))
{
++it; // skip @
Expand Down Expand Up @@ -387,9 +376,9 @@ inline void format_sam_base::read_header(stream_view_type && stream_view,
header_entry = std::addressof(hdr.grouping);
break;
}
default: // unsupported header tag
default: // unknown/user tag
{
consume_unsupported_tag_and_print_warning("HD", raw_tag);
parse_and_append_unhandled_tag_to_string(hdr.user_tags, raw_tag);
}
}

Expand Down Expand Up @@ -561,7 +550,7 @@ inline void format_sam_base::read_header(stream_view_type && stream_view,
}
default: // unsupported header tag
{
consume_unsupported_tag_and_print_warning("PG", raw_tag);
parse_and_append_unhandled_tag_to_string(tmp.user_tags, raw_tag);
}
}

Expand Down Expand Up @@ -665,6 +654,9 @@ format_sam_base::write_header(stream_t & stream, sam_file_output_options const &
if (!header.grouping.empty())
stream << "\tGO:" << header.grouping;

if (!header.user_tags.empty())
stream << '\t' << header.user_tags;

detail::write_eol(stream_it, options.add_carriage_return);

// (@SQ) Write Reference Sequence Dictionary lines [required].
Expand Down Expand Up @@ -715,6 +707,9 @@ format_sam_base::write_header(stream_t & stream, sam_file_output_options const &
if (!program.version.empty())
stream << "\tVN:" << program.version;

if (!program.user_tags.empty())
stream << '\t' << program.user_tags;

detail::write_eol(stream_it, options.add_carriage_return);
}

Expand Down
3 changes: 3 additions & 0 deletions include/seqan3/io/sam_file/header.hpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@ struct sam_file_program_info_t
std::string previous; //!< The id of the previous program if program calls were chained.
std::string description; //!< A description of the program and/or program call.
std::string version; //!< The program/tool version.
std::string user_tags; //!< Additional user-defined tags.
};

/*!\brief Stores the header information of SAM/BAM files.
Expand Down Expand Up @@ -213,6 +214,8 @@ class sam_file_header
* * **SM:** Sample. Use pool name where a pool is being sequenced.
*/
std::vector<std::pair<std::string, std::string>> read_groups;

std::string user_tags; //!< Additional user-defined tags.
};

} // namespace seqan3
110 changes: 62 additions & 48 deletions test/unit/io/sam_file/format_bam_test.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -38,14 +38,24 @@ struct sam_file_read<seqan3::format_bam> : public sam_file_data
'\x72', '\x65', '\x66', '\x00', '\x22', '\x00', '\x00', '\x00'};

std::string unknown_tag_header{
'\x42', '\x41', '\x4d', '\x01', '\x4b', '\x00', '\x00', '\x00', '\x40', '\x48', '\x44', '\x09', '\x56',
'\x4e', '\x3a', '\x31', '\x2e', '\x36', '\x09', '\x70', '\x62', '\x3a', '\x35', '\x2e', '\x30', '\x2e',
'\x30', '\x09', '\x6f', '\x74', '\x74', '\x65', '\x72', '\x0a', '\x40', '\x53', '\x51', '\x09', '\x53',
'\x4e', '\x3a', '\x72', '\x65', '\x66', '\x09', '\x4c', '\x4e', '\x3a', '\x33', '\x34', '\x0a', '\x40',
'\x50', '\x47', '\x09', '\x49', '\x44', '\x3a', '\x6e', '\x6f', '\x76', '\x6f', '\x61', '\x6c', '\x69',
'\x67', '\x6e', '\x09', '\x70', '\x62', '\x3a', '\x35', '\x2e', '\x30', '\x2e', '\x30', '\x09', '\x6f',
'\x74', '\x74', '\x65', '\x72', '\x0a', '\x01', '\x00', '\x00', '\x00', '\x04', '\x00', '\x00', '\x00',
'\x72', '\x65', '\x66', '\x00', '\x22', '\x00', '\x00', '\x00'};
'\x42', '\x41', '\x4d', '\x01', '\xe3', '\x00', '\x00', '\x00', '\x40', '\x48', '\x44', '\x09', '\x56', '\x4e',
'\x3a', '\x31', '\x2e', '\x36', '\x09', '\x70', '\x62', '\x3a', '\x35', '\x2e', '\x30', '\x2e', '\x30', '\x09',
'\x6f', '\x74', '\x74', '\x65', '\x72', '\x0a', '\x40', '\x53', '\x51', '\x09', '\x53', '\x4e', '\x3a', '\x72',
'\x65', '\x66', '\x09', '\x4c', '\x4e', '\x3a', '\x33', '\x34', '\x09', '\x70', '\x62', '\x3a', '\x35', '\x2e',
'\x30', '\x2e', '\x30', '\x09', '\x6f', '\x74', '\x74', '\x65', '\x72', '\x0a', '\x40', '\x52', '\x47', '\x09',
'\x49', '\x44', '\x3a', '\x52', '\x31', '\x09', '\x70', '\x62', '\x3a', '\x35', '\x2e', '\x30', '\x2e', '\x30',
'\x09', '\x6f', '\x74', '\x74', '\x65', '\x72', '\x0a', '\x40', '\x50', '\x47', '\x09', '\x49', '\x44', '\x3a',
'\x6e', '\x6f', '\x76', '\x6f', '\x61', '\x6c', '\x69', '\x67', '\x6e', '\x09', '\x70', '\x62', '\x3a', '\x35',
'\x2e', '\x30', '\x2e', '\x30', '\x09', '\x6f', '\x74', '\x74', '\x65', '\x72', '\x0a', '\x40', '\x50', '\x47',
'\x09', '\x49', '\x44', '\x3a', '\x73', '\x61', '\x6d', '\x74', '\x6f', '\x6f', '\x6c', '\x73', '\x09', '\x50',
'\x4e', '\x3a', '\x73', '\x61', '\x6d', '\x74', '\x6f', '\x6f', '\x6c', '\x73', '\x09', '\x50', '\x50', '\x3a',
'\x6e', '\x6f', '\x76', '\x6f', '\x61', '\x6c', '\x69', '\x67', '\x6e', '\x09', '\x56', '\x4e', '\x3a', '\x31',
'\x2e', '\x31', '\x33', '\x09', '\x43', '\x4c', '\x3a', '\x73', '\x61', '\x6d', '\x74', '\x6f', '\x6f', '\x6c',
'\x73', '\x20', '\x76', '\x69', '\x65', '\x77', '\x20', '\x2d', '\x48', '\x20', '\x2d', '\x62', '\x20', '\x2f',
'\x68', '\x6f', '\x6d', '\x65', '\x2f', '\x69', '\x6e', '\x66', '\x72', '\x69', '\x2f', '\x64', '\x65', '\x76',
'\x65', '\x6c', '\x6f', '\x70', '\x2f', '\x73', '\x65', '\x71', '\x61', '\x6e', '\x33', '\x2f', '\x74', '\x65',
'\x73', '\x74', '\x2e', '\x73', '\x61', '\x6d', '\x0a', '\x01', '\x00', '\x00', '\x00', '\x04', '\x00', '\x00',
'\x00', '\x72', '\x65', '\x66', '\x00', '\x22', '\x00', '\x00', '\x00'};

std::string big_header_input{
'\x42', '\x41', '\x4D', '\x01', '\xB7', '\x01', '\x00', '\x00', '\x40', '\x48', '\x44', '\x09', '\x56', '\x4E',
Expand Down Expand Up @@ -316,47 +326,51 @@ struct sam_file_read<seqan3::format_bam> : public sam_file_data
'\x66', '\x66', '\x66', '\x46', '\x40', '\x7A', '\x7A', '\x5A', '\x73', '\x74', '\x72', '\x00', '\x0A'};

std::string verbose_output{
'\x42', '\x41', '\x4d', '\x01', '\xa6', '\x00', '\x00', '\x00', '\x40', '\x48', '\x44', '\x09', '\x56', '\x4e',
'\x42', '\x41', '\x4d', '\x01', '\xe2', '\x00', '\x00', '\x00', '\x40', '\x48', '\x44', '\x09', '\x56', '\x4e',
'\x3a', '\x31', '\x2e', '\x36', '\x09', '\x53', '\x4f', '\x3a', '\x75', '\x6e', '\x6b', '\x6e', '\x6f', '\x77',
'\x6e', '\x09', '\x47', '\x4f', '\x3a', '\x6e', '\x6f', '\x6e', '\x65', '\x0a', '\x40', '\x53', '\x51', '\x09',
'\x53', '\x4e', '\x3a', '\x72', '\x65', '\x66', '\x09', '\x4c', '\x4e', '\x3a', '\x33', '\x34', '\x09', '\x41',
'\x4e', '\x3a', '\x6f', '\x74', '\x68', '\x65', '\x72', '\x5f', '\x6e', '\x61', '\x6d', '\x65', '\x0a', '\x40',
'\x52', '\x47', '\x09', '\x49', '\x44', '\x3a', '\x67', '\x72', '\x6f', '\x75', '\x70', '\x31', '\x09', '\x44',
'\x53', '\x3a', '\x6d', '\x6f', '\x72', '\x65', '\x20', '\x69', '\x6e', '\x66', '\x6f', '\x0a', '\x40', '\x50',
'\x47', '\x09', '\x49', '\x44', '\x3a', '\x70', '\x72', '\x6f', '\x67', '\x31', '\x09', '\x50', '\x4e', '\x3a',
'\x63', '\x6f', '\x6f', '\x6c', '\x5f', '\x70', '\x72', '\x6f', '\x67', '\x72', '\x61', '\x6d', '\x09', '\x43',
'\x4c', '\x3a', '\x2e', '\x2f', '\x70', '\x72', '\x6f', '\x67', '\x31', '\x09', '\x50', '\x50', '\x3a', '\x61',
'\x09', '\x44', '\x53', '\x3a', '\x62', '\x09', '\x56', '\x4e', '\x3a', '\x63', '\x0a', '\x40', '\x43', '\x4f',
'\x09', '\x54', '\x68', '\x69', '\x73', '\x20', '\x69', '\x73', '\x20', '\x61', '\x20', '\x63', '\x6f', '\x6d',
'\x6d', '\x65', '\x6e', '\x74', '\x2e', '\x0a', '\x01', '\x00', '\x00', '\x00', '\x04', '\x00', '\x00', '\x00',
'\x72', '\x65', '\x66', '\x00', '\x22', '\x00', '\x00', '\x00', '\x64', '\x00', '\x00', '\x00', '\x00', '\x00',
'\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x06', '\x3d', '\x49', '\x12', '\x05', '\x00', '\x29', '\x00',
'\x04', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x09', '\x00', '\x00', '\x00', '\x2c', '\x01',
'\x00', '\x00', '\x72', '\x65', '\x61', '\x64', '\x31', '\x00', '\x14', '\x00', '\x00', '\x00', '\x10', '\x00',
'\x00', '\x00', '\x12', '\x00', '\x00', '\x00', '\x10', '\x00', '\x00', '\x00', '\x11', '\x00', '\x00', '\x00',
'\x12', '\x48', '\x00', '\x02', '\x02', '\x03', '\x41', '\x53', '\x43', '\x02', '\x43', '\x43', '\x53', '\x2c',
'\x01', '\x4e', '\x4d', '\x63', '\xf9', '\x61', '\x61', '\x41', '\x63', '\x63', '\x63', '\x73', '\xd4', '\xfe',
'\x66', '\x66', '\x66', '\x66', '\x66', '\x46', '\x40', '\x7a', '\x7a', '\x5a', '\x73', '\x74', '\x72', '\x00',
'\xaf', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x01', '\x00', '\x00', '\x00', '\x06', '\x3e',
'\x49', '\x12', '\x06', '\x00', '\x2a', '\x00', '\x09', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00',
'\x09', '\x00', '\x00', '\x00', '\x2c', '\x01', '\x00', '\x00', '\x72', '\x65', '\x61', '\x64', '\x32', '\x00',
'\x15', '\x00', '\x00', '\x00', '\x70', '\x00', '\x00', '\x00', '\x12', '\x00', '\x00', '\x00', '\x10', '\x00',
'\x00', '\x00', '\x14', '\x00', '\x00', '\x00', '\x25', '\x00', '\x00', '\x00', '\x14', '\x42', '\x84', '\xf1',
'\x40', '\x00', '\x02', '\x02', '\x03', '\x05', '\x06', '\x07', '\x08', '\x09', '\x62', '\x43', '\x42', '\x43',
'\x02', '\x00', '\x00', '\x00', '\x03', '\xc8', '\x62', '\x49', '\x42', '\x49', '\x01', '\x00', '\x00', '\x00',
'\x00', '\xd8', '\x94', '\x11', '\x62', '\x53', '\x42', '\x53', '\x03', '\x00', '\x00', '\x00', '\x2c', '\x01',
'\x28', '\x00', '\xf4', '\x01', '\x62', '\x63', '\x42', '\x63', '\x01', '\x00', '\x00', '\x00', '\xfd', '\x62',
'\x66', '\x42', '\x66', '\x03', '\x00', '\x00', '\x00', '\x00', '\x00', '\x60', '\x40', '\xcd', '\xcc', '\xcc',
'\x3d', '\x33', '\x33', '\x2f', '\x42', '\x62', '\x69', '\x42', '\x69', '\x03', '\x00', '\x00', '\x00', '\xfd',
'\xff', '\xff', '\xff', '\xc8', '\x00', '\x00', '\x00', '\x30', '\xfe', '\xfe', '\xff', '\x62', '\x73', '\x42',
'\x73', '\x03', '\x00', '\x00', '\x00', '\xfd', '\xff', '\xc8', '\x00', '\xd4', '\xfe', '\x5a', '\x00', '\x00',
'\x00', '\x00', '\x00', '\x00', '\x00', '\x02', '\x00', '\x00', '\x00', '\x06', '\x3f', '\x49', '\x12', '\x0a',
'\x00', '\x2b', '\x00', '\x08', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x09', '\x00', '\x00',
'\x00', '\x2c', '\x01', '\x00', '\x00', '\x72', '\x65', '\x61', '\x64', '\x33', '\x00', '\x14', '\x00', '\x00',
'\x00', '\x10', '\x00', '\x00', '\x00', '\x16', '\x00', '\x00', '\x00', '\x10', '\x00', '\x00', '\x00', '\x11',
'\x00', '\x00', '\x00', '\x10', '\x00', '\x00', '\x00', '\x11', '\x00', '\x00', '\x00', '\x12', '\x00', '\x00',
'\x00', '\x10', '\x00', '\x00', '\x00', '\x14', '\x00', '\x00', '\x00', '\x44', '\x14', '\x81', '\x81', '\x00',
'\x00', '\x09', '\x0a', '\x0b', '\x0c', '\x0d', '\x0e'};
'\x6e', '\x09', '\x47', '\x4f', '\x3a', '\x6e', '\x6f', '\x6e', '\x65', '\x09', '\x70', '\x62', '\x3a', '\x35',
'\x2e', '\x30', '\x2e', '\x30', '\x09', '\x6f', '\x74', '\x74', '\x65', '\x72', '\x0a', '\x40', '\x53', '\x51',
'\x09', '\x53', '\x4e', '\x3a', '\x72', '\x65', '\x66', '\x09', '\x4c', '\x4e', '\x3a', '\x33', '\x34', '\x09',
'\x41', '\x4e', '\x3a', '\x6f', '\x74', '\x68', '\x65', '\x72', '\x5f', '\x6e', '\x61', '\x6d', '\x65', '\x09',
'\x70', '\x62', '\x3a', '\x35', '\x2e', '\x30', '\x2e', '\x30', '\x09', '\x6f', '\x74', '\x74', '\x65', '\x72',
'\x0a', '\x40', '\x52', '\x47', '\x09', '\x49', '\x44', '\x3a', '\x67', '\x72', '\x6f', '\x75', '\x70', '\x31',
'\x09', '\x44', '\x53', '\x3a', '\x6d', '\x6f', '\x72', '\x65', '\x20', '\x69', '\x6e', '\x66', '\x6f', '\x09',
'\x70', '\x62', '\x3a', '\x35', '\x2e', '\x30', '\x2e', '\x30', '\x09', '\x6f', '\x74', '\x74', '\x65', '\x72',
'\x0a', '\x40', '\x50', '\x47', '\x09', '\x49', '\x44', '\x3a', '\x70', '\x72', '\x6f', '\x67', '\x31', '\x09',
'\x50', '\x4e', '\x3a', '\x63', '\x6f', '\x6f', '\x6c', '\x5f', '\x70', '\x72', '\x6f', '\x67', '\x72', '\x61',
'\x6d', '\x09', '\x43', '\x4c', '\x3a', '\x2e', '\x2f', '\x70', '\x72', '\x6f', '\x67', '\x31', '\x09', '\x50',
'\x50', '\x3a', '\x61', '\x09', '\x44', '\x53', '\x3a', '\x62', '\x09', '\x56', '\x4e', '\x3a', '\x63', '\x09',
'\x70', '\x62', '\x3a', '\x35', '\x2e', '\x30', '\x2e', '\x30', '\x09', '\x6f', '\x74', '\x74', '\x65', '\x72',
'\x0a', '\x40', '\x43', '\x4f', '\x09', '\x54', '\x68', '\x69', '\x73', '\x20', '\x69', '\x73', '\x20', '\x61',
'\x20', '\x63', '\x6f', '\x6d', '\x6d', '\x65', '\x6e', '\x74', '\x2e', '\x0a', '\x01', '\x00', '\x00', '\x00',
'\x04', '\x00', '\x00', '\x00', '\x72', '\x65', '\x66', '\x00', '\x22', '\x00', '\x00', '\x00', '\x64', '\x00',
'\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x06', '\x3d', '\x49', '\x12',
'\x05', '\x00', '\x29', '\x00', '\x04', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x09', '\x00',
'\x00', '\x00', '\x2c', '\x01', '\x00', '\x00', '\x72', '\x65', '\x61', '\x64', '\x31', '\x00', '\x14', '\x00',
'\x00', '\x00', '\x10', '\x00', '\x00', '\x00', '\x12', '\x00', '\x00', '\x00', '\x10', '\x00', '\x00', '\x00',
'\x11', '\x00', '\x00', '\x00', '\x12', '\x48', '\x00', '\x02', '\x02', '\x03', '\x41', '\x53', '\x43', '\x02',
'\x43', '\x43', '\x53', '\x2c', '\x01', '\x4e', '\x4d', '\x63', '\xf9', '\x61', '\x61', '\x41', '\x63', '\x63',
'\x63', '\x73', '\xd4', '\xfe', '\x66', '\x66', '\x66', '\x66', '\x66', '\x46', '\x40', '\x7a', '\x7a', '\x5a',
'\x73', '\x74', '\x72', '\x00', '\xaf', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x01', '\x00',
'\x00', '\x00', '\x06', '\x3e', '\x49', '\x12', '\x06', '\x00', '\x2a', '\x00', '\x09', '\x00', '\x00', '\x00',
'\x00', '\x00', '\x00', '\x00', '\x09', '\x00', '\x00', '\x00', '\x2c', '\x01', '\x00', '\x00', '\x72', '\x65',
'\x61', '\x64', '\x32', '\x00', '\x15', '\x00', '\x00', '\x00', '\x70', '\x00', '\x00', '\x00', '\x12', '\x00',
'\x00', '\x00', '\x10', '\x00', '\x00', '\x00', '\x14', '\x00', '\x00', '\x00', '\x25', '\x00', '\x00', '\x00',
'\x14', '\x42', '\x84', '\xf1', '\x40', '\x00', '\x02', '\x02', '\x03', '\x05', '\x06', '\x07', '\x08', '\x09',
'\x62', '\x43', '\x42', '\x43', '\x02', '\x00', '\x00', '\x00', '\x03', '\xc8', '\x62', '\x49', '\x42', '\x49',
'\x01', '\x00', '\x00', '\x00', '\x00', '\xd8', '\x94', '\x11', '\x62', '\x53', '\x42', '\x53', '\x03', '\x00',
'\x00', '\x00', '\x2c', '\x01', '\x28', '\x00', '\xf4', '\x01', '\x62', '\x63', '\x42', '\x63', '\x01', '\x00',
'\x00', '\x00', '\xfd', '\x62', '\x66', '\x42', '\x66', '\x03', '\x00', '\x00', '\x00', '\x00', '\x00', '\x60',
'\x40', '\xcd', '\xcc', '\xcc', '\x3d', '\x33', '\x33', '\x2f', '\x42', '\x62', '\x69', '\x42', '\x69', '\x03',
'\x00', '\x00', '\x00', '\xfd', '\xff', '\xff', '\xff', '\xc8', '\x00', '\x00', '\x00', '\x30', '\xfe', '\xfe',
'\xff', '\x62', '\x73', '\x42', '\x73', '\x03', '\x00', '\x00', '\x00', '\xfd', '\xff', '\xc8', '\x00', '\xd4',
'\xfe', '\x5a', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x02', '\x00', '\x00', '\x00', '\x06',
'\x3f', '\x49', '\x12', '\x0a', '\x00', '\x2b', '\x00', '\x08', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00',
'\x00', '\x09', '\x00', '\x00', '\x00', '\x2c', '\x01', '\x00', '\x00', '\x72', '\x65', '\x61', '\x64', '\x33',
'\x00', '\x14', '\x00', '\x00', '\x00', '\x10', '\x00', '\x00', '\x00', '\x16', '\x00', '\x00', '\x00', '\x10',
'\x00', '\x00', '\x00', '\x11', '\x00', '\x00', '\x00', '\x10', '\x00', '\x00', '\x00', '\x11', '\x00', '\x00',
'\x00', '\x12', '\x00', '\x00', '\x00', '\x10', '\x00', '\x00', '\x00', '\x14', '\x00', '\x00', '\x00', '\x44',
'\x14', '\x81', '\x81', '\x00', '\x00', '\x09', '\x0a', '\x0b', '\x0c', '\x0d', '\x0e'};

std::string special_output{
'\x42', '\x41', '\x4D', '\x01', '\x1C', '\x00', '\x00', '\x00', '\x40', '\x48', '\x44', '\x09', '\x56', '\x4E',
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11 changes: 6 additions & 5 deletions test/unit/io/sam_file/format_sam_test.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,8 @@ struct sam_file_read<seqan3::format_sam> : public sam_file_data
// However, encountering such a tag should not break the parsing.
std::string unknown_tag_header{
R"(@HD VN:1.6 pb:5.0.0 otter
@SQ SN:ref LN:34
@SQ SN:ref LN:34 pb:5.0.0 otter
@RG ID:R1 pb:5.0.0 otter
@PG ID:novoalign pb:5.0.0 otter
)"};

Expand Down Expand Up @@ -87,10 +88,10 @@ read3 43 ref 3 63 1S1M1P1M1I1M1I1D1M1S ref 10 300 GGAGTATA !!*+,-./
// -----------------------------------------------------------------------------------------------------------------

std::string verbose_output{
R"(@HD VN:1.6 SO:unknown GO:none
@SQ SN:ref LN:34 AN:other_name
@RG ID:group1 DS:more info
@PG ID:prog1 PN:cool_program CL:./prog1 PP:a DS:b VN:c
R"(@HD VN:1.6 SO:unknown GO:none pb:5.0.0 otter
@SQ SN:ref LN:34 AN:other_name pb:5.0.0 otter
@RG ID:group1 DS:more info pb:5.0.0 otter
@PG ID:prog1 PN:cool_program CL:./prog1 PP:a DS:b VN:c pb:5.0.0 otter
@CO This is a comment.
read1 41 ref 1 61 1S1M1D1M1I ref 10 300 ACGT !##$ AS:i:2 CC:i:300 NM:i:-7 aa:A:c cc:i:-300 ff:f:3.1 zz:Z:str
read2 42 ref 2 62 1H7M1D1M1S2H ref 10 300 AGGCTGNAG !##$&'()* bC:B:C,3,200 bI:B:I,294967296 bS:B:S,300,40,500 bc:B:c,-3 bf:B:f,3.5,0.1,43.8 bi:B:i,-3,200,-66000 bs:B:s,-3,200,-300
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