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[MISC] Revert tag handling
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@eseiler
eseiler committed Jun 3, 2024
1 parent 21c7d04 commit da6a491
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Showing 11 changed files with 50 additions and 277 deletions.
12 changes: 4 additions & 8 deletions include/seqan3/io/sam_file/detail/format_sam_base.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,6 @@
#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>
Expand Down Expand Up @@ -83,11 +82,10 @@ 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, typename seq_legal_alph_type>
template <typename stream_view_type, typename ref_ids_type, typename ref_seqs_type>
void read_header(stream_view_type && stream_view,
sam_file_header<ref_ids_type> & hdr,
ref_seqs_type & /*ref_id_to_pos_map*/,
sam_file_input_options<seq_legal_alph_type> const & options);
ref_seqs_type & /*ref_id_to_pos_map*/);

template <typename stream_t, typename header_type>
void write_header(stream_t & stream, sam_file_output_options const & options, header_type & header);
Expand Down Expand Up @@ -260,7 +258,6 @@ inline void format_sam_base::read_arithmetic_field(std::string_view const & str,
* \tparam stream_view_type The type of the stream as a view.
* \param[in, out] stream_view The stream view to iterate over.
* \param[in, out] hdr The header (as a pointer) to store the parsed values.
* \param[in] options The options to alter the parsing process.
*
* \throws seqan3::format_error if any unexpected character or format is encountered.
*
Expand All @@ -275,11 +272,10 @@ inline void format_sam_base::read_arithmetic_field(std::string_view const & str,
* 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.
*/
template <typename stream_view_type, typename ref_ids_type, typename ref_seqs_type, typename seq_legal_alph_type>
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,
sam_file_header<ref_ids_type> & hdr,
ref_seqs_type & /*ref_id_to_pos_map*/,
sam_file_input_options<seq_legal_alph_type> const & options)
ref_seqs_type & /*ref_id_to_pos_map*/)
{
auto it = std::ranges::begin(stream_view);
auto end = std::ranges::end(stream_view);
Expand Down
41 changes: 21 additions & 20 deletions include/seqan3/io/sam_file/format_bam.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -84,7 +84,7 @@ class format_bam : private detail::format_sam_base
typename e_value_type,
typename bit_score_type>
void read_alignment_record(stream_type & stream,
sam_file_input_options<seq_legal_alph_type> const & options,
sam_file_input_options<seq_legal_alph_type> const & SEQAN3_DOXYGEN_ONLY(options),
ref_seqs_type & ref_seqs,
sam_file_header<ref_ids_type> & header,
stream_pos_type & position_buffer,
Expand Down Expand Up @@ -261,24 +261,25 @@ template <typename stream_type, // constraints checked by file
typename tag_dict_type,
typename e_value_type,
typename bit_score_type>
inline void format_bam::read_alignment_record(stream_type & stream,
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,
seq_type & seq,
qual_type & qual,
id_type & id,
ref_seq_type & SEQAN3_DOXYGEN_ONLY(ref_seq),
ref_id_type & ref_id,
ref_offset_type & ref_offset,
cigar_type & cigar_vector,
flag_type & flag,
mapq_type & mapq,
mate_type & mate,
tag_dict_type & tag_dict,
e_value_type & SEQAN3_DOXYGEN_ONLY(e_value),
bit_score_type & SEQAN3_DOXYGEN_ONLY(bit_score))
inline void
format_bam::read_alignment_record(stream_type & stream,
sam_file_input_options<seq_legal_alph_type> const & SEQAN3_DOXYGEN_ONLY(options),
ref_seqs_type & ref_seqs,
sam_file_header<ref_ids_type> & header,
stream_pos_type & position_buffer,
seq_type & seq,
qual_type & qual,
id_type & id,
ref_seq_type & SEQAN3_DOXYGEN_ONLY(ref_seq),
ref_id_type & ref_id,
ref_offset_type & ref_offset,
cigar_type & cigar_vector,
flag_type & flag,
mapq_type & mapq,
mate_type & mate,
tag_dict_type & tag_dict,
e_value_type & SEQAN3_DOXYGEN_ONLY(e_value),
bit_score_type & SEQAN3_DOXYGEN_ONLY(bit_score))
{
static_assert(detail::decays_to_ignore_v<ref_offset_type>
|| detail::is_type_specialisation_of_v<ref_offset_type, std::optional>,
Expand Down Expand Up @@ -308,7 +309,7 @@ inline void 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, options);
read_header(stream_view | detail::take_exactly_or_throw(l_text), header, ref_seqs);

read_integral_byte_field(stream_view, n_ref);

Expand Down
41 changes: 21 additions & 20 deletions include/seqan3/io/sam_file/format_sam.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -165,7 +165,7 @@ class format_sam : protected detail::format_sam_base
typename e_value_type,
typename bit_score_type>
void read_alignment_record(stream_type & stream,
sam_file_input_options<seq_legal_alph_type> const & options,
sam_file_input_options<seq_legal_alph_type> const & SEQAN3_DOXYGEN_ONLY(options),
ref_seqs_type & ref_seqs,
sam_file_header<ref_ids_type> & header,
stream_pos_type & position_buffer,
Expand Down Expand Up @@ -354,24 +354,25 @@ template <typename stream_type, // constraints checked by file
typename tag_dict_type,
typename e_value_type,
typename bit_score_type>
inline void format_sam::read_alignment_record(stream_type & stream,
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,
seq_type & seq,
qual_type & qual,
id_type & id,
ref_seq_type & SEQAN3_DOXYGEN_ONLY(ref_seq),
ref_id_type & ref_id,
ref_offset_type & ref_offset,
cigar_type & cigar_vector,
flag_type & flag,
mapq_type & mapq,
mate_type & mate,
tag_dict_type & tag_dict,
e_value_type & SEQAN3_DOXYGEN_ONLY(e_value),
bit_score_type & SEQAN3_DOXYGEN_ONLY(bit_score))
inline void
format_sam::read_alignment_record(stream_type & stream,
sam_file_input_options<seq_legal_alph_type> const & SEQAN3_DOXYGEN_ONLY(options),
ref_seqs_type & ref_seqs,
sam_file_header<ref_ids_type> & header,
stream_pos_type & position_buffer,
seq_type & seq,
qual_type & qual,
id_type & id,
ref_seq_type & SEQAN3_DOXYGEN_ONLY(ref_seq),
ref_id_type & ref_id,
ref_offset_type & ref_offset,
cigar_type & cigar_vector,
flag_type & flag,
mapq_type & mapq,
mate_type & mate,
tag_dict_type & tag_dict,
e_value_type & SEQAN3_DOXYGEN_ONLY(e_value),
bit_score_type & SEQAN3_DOXYGEN_ONLY(bit_score))
{
static_assert(detail::decays_to_ignore_v<ref_offset_type>
|| detail::is_type_specialisation_of_v<ref_offset_type, std::optional>,
Expand All @@ -388,7 +389,7 @@ inline void 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, options);
read_header(stream_view, header, ref_seqs);

if (std::ranges::begin(stream_view) == std::ranges::end(stream_view)) // file has no records
return;
Expand Down
16 changes: 1 addition & 15 deletions include/seqan3/io/sam_file/input_options.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,6 @@

#pragma once

#include <iostream>

#include <seqan3/core/platform.hpp>

namespace seqan3
Expand All @@ -23,18 +21,6 @@ namespace seqan3
*/
template <typename sequence_legal_alphabet>
struct sam_file_input_options
{
/*!\brief The stream to write warnings to. Defaults to std::cerr.
* \details
* ### Example
* \include test/snippet/io/sam_file/sam_file_input_options.cpp
* Output to std::cerr:
* \include test/snippet/io/sam_file/sam_file_input_options.err
* Output to std::cout:
* \include test/snippet/io/sam_file/sam_file_input_options.out
* \experimentalapi{Experimental since version 3.4.}
*/
std::ostream * stream_warnings_to{std::addressof(std::cerr)};
};
{};

} // namespace seqan3
114 changes: 0 additions & 114 deletions test/snippet/io/sam_file/sam_file_input_options.cpp
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8 changes: 0 additions & 8 deletions test/snippet/io/sam_file/sam_file_input_options.err
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3 changes: 0 additions & 3 deletions test/snippet/io/sam_file/sam_file_input_options.err.license
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10 changes: 0 additions & 10 deletions test/snippet/io/sam_file/sam_file_input_options.out
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3 changes: 0 additions & 3 deletions test/snippet/io/sam_file/sam_file_input_options.out.license
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14 changes: 2 additions & 12 deletions test/unit/io/sam_file/format_sam_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -173,29 +173,19 @@ TEST_F(sam_format, header_errors)
seqan3::sam_file_input fin{istream, seqan3::format_sam{}};
EXPECT_NO_THROW(fin.begin());
}
{ // user defined tags should not trigger errors, but print warnings to cerr
{ // user defined tags should not trigger errors
std::string header_str{
"@HD\tVN:1.6\tVB:user_tag\tSB:user_tag\tGB:user_tag\tpb:user_tag\n"
"@SQ\tSN:ref2\tLN:243199373\tSB:user_tag\tLB:user_tag\tpb:user_tag\n"
"@RG\tID:U0a_A2_L1\tIB:user_tag\tpb:user_tag\n"
"@PG\tID:qc\tIB:user_tag\tPB:user_tag\tCB:user_tag\tDB:user_tag\tVB:user_tag\tpb:user_tag\n"};
std::string expected_cerr{"Unsupported tag found in SAM header @HD: \"VB:user_tag\"\n"
"Unsupported tag found in SAM header @HD: \"SB:user_tag\"\n"
"Unsupported tag found in SAM header @HD: \"GB:user_tag\"\n"
"Unsupported tag found in SAM header @HD: \"pb:user_tag\"\n"
"Unsupported tag found in SAM header @PG: \"IB:user_tag\"\n"
"Unsupported tag found in SAM header @PG: \"PB:user_tag\"\n"
"Unsupported tag found in SAM header @PG: \"CB:user_tag\"\n"
"Unsupported tag found in SAM header @PG: \"DB:user_tag\"\n"
"Unsupported tag found in SAM header @PG: \"VB:user_tag\"\n"
"Unsupported tag found in SAM header @PG: \"pb:user_tag\"\n"};

std::istringstream istream(header_str);
seqan3::sam_file_input fin{istream, seqan3::format_sam{}};

testing::internal::CaptureStderr();
EXPECT_NO_THROW(fin.begin());
EXPECT_EQ(testing::internal::GetCapturedStderr(), expected_cerr);
EXPECT_EQ(testing::internal::GetCapturedStderr(), "");
}
{ // missing VN tag in @HD
std::string header_str{"@HD\n"};
Expand Down
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