remove ref_seq, evalue, bit_score from sam file output #2658
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marehr
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a team and
MitraDarja
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…_seq, evalue, bit_score}) sam_file_output does not need the fields ref_seq, evalue, bit_score. This commit remove those fields from the default-fields and ensures that custom fields don't contain those fields. This commit also splits ::push_back and ::emplace_back into four versions to deprecate the usage of the old default-fields case.
…seq, evalue, bit_score})
Codecov Report
@@ Coverage Diff @@
## release-3.0.3 #2658 +/- ##
==============================================
Coverage 98.22% 98.22%
==============================================
Files 276 276
Lines 10810 10831 +21
==============================================
+ Hits 10618 10639 +21
Misses 192 192
Continue to review full report at Codecov.
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TODO: Changelog |
MitraDarja
approved these changes
May 17, 2021
Comment on lines
547
to
554
| // new syntax enforces via static_assert that field::ref_seq, field::evalue, and field::bit_score isn't set | ||
| requires tuple_like<tuple_t> && (!detail::record_like<tuple_t>) && (!is_default_selected_field_ids) | ||
| //!\endcond | ||
| { | ||
| push_back_tuple(std::forward<tuple_t>(t)); | ||
| } | ||
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| // This is a bit of a problem, because to decide whether the new syntax or the old syntax is used is a bit |
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The comments here are a bit confusing. I would suggest:
Suggested change
| // new syntax enforces via static_assert that field::ref_seq, field::evalue, and field::bit_score isn't set | |
| requires tuple_like<tuple_t> && (!detail::record_like<tuple_t>) && (!is_default_selected_field_ids) | |
| //!\endcond | |
| { | |
| push_back_tuple(std::forward<tuple_t>(t)); | |
| } | |
| // This is a bit of a problem, because to decide whether the new syntax or the old syntax is used is a bit | |
| // The new syntax enforces via static_assert (see above) that field::ref_seq, field::evalue, and field::bit_score isn't set. This causes a problem, because it is complicated to decide whether the new syntax or the old syntax is used. |
marehr
commented
May 17, 2021
marehr
commented
May 17, 2021
eseiler
approved these changes
May 19, 2021
|
squash or rebase? |
eseiler
added a commit
that referenced
this pull request
May 19, 2021
* [TEST] move debug_stream_alignment_test.cpp * [TEST] move cigar_operation_test.cpp * [TEST] add alphabet/range/hash_test.cpp * [TEST] move buffer_queue_test.cpp * [TEST] move inherited_iterator_base_test.cpp * [TEST] move random_access_iterator_test.cpp * [TEST] move istreambuf_view_test.cpp * [TEST] add io/detail/magic_header_test.cpp * [TEST] add io/detail/take_exactly_view_test.cpp * [TEST] move char_operations_predicate_test.cpp * [TEST] move integer_traits_test.cpp * [TEST] move type_name_as_string_test.cpp * [TEST] move transformation_trait_or_test.cpp * [TEST] move convert_test.cpp * [TEST] move deep_test.cpp * [DOC] fix snippet * [INFRA] update platform.hpp * [FIX] remove unnecessary includes * [MISC] update ranges-library and remove workaround * [INFRA] add -DCMAKE_BUILD_TYPE=FEDORA to simulate fedora builds * [INFRA] automatically generate snippets from a scaffold * [DOC] generate all [rd]na(4|5|15)_implicit_conversion_from_[rd]na(4|5|15).cpp snippets * [DOC] re-generate all [rd]na(4|5|15)(_char|)_literal * [DOC] make sure implict conversion is as expected * [INFRA] Ignore apt failures * Check changelog links and add header changes. (#2641) * Check changelog links and add header changes. * reordering * Add missed headers. and remove detail headers. all.hpp's are not included. * Update CHANGELOG.md Co-authored-by: Lydia Buntrock <[email protected]> * Update CHANGELOG.md Co-authored-by: Lydia Buntrock <[email protected]> * Update CHANGELOG.md Co-authored-by: Lydia Buntrock <[email protected]> * Update CHANGELOG.md Co-authored-by: Lydia Buntrock <[email protected]> * Apply 2nd review. Co-authored-by: Lydia Buntrock <[email protected]> * [DOC] Move changelog entries to their correct place (from 3.0.2 to 3.0.3) * [DOC] add known good compilers to CHANGELOG.md * [DOC] fix links in CHANGELOG.md * [FIX] brew script * [DOC] add documentation for CentOS 7 / RHEL 7 (#2661) * [DOC] add documentation for CentOS 7 / RHEL 7 Fixes #2244 (comment) * [skip ci] * Apply suggestions from code review Co-authored-by: Enrico Seiler <[email protected]> Co-authored-by: Enrico Seiler <[email protected]> * remove ref_seq, evalue, bit_score from sam file output (#2658) * [MISC] deprecate seqan3::sam_file::output fields (seqan3::field::{ref_seq, evalue, bit_score}) sam_file_output does not need the fields ref_seq, evalue, bit_score. This commit remove those fields from the default-fields and ensures that custom fields don't contain those fields. This commit also splits ::push_back and ::emplace_back into four versions to deprecate the usage of the old default-fields case. * [MISC] deprecate seqan3::sam_file_output::{emplace, push}_back * [MISC] deprecate seqan3::sam_file::input fields (seqan3::field::{ref_seq, evalue, bit_score}) * [MISC] fix gcc-7 issues with SEQAN3_DEPRECATED_310 * [FIX] remove seqan3::field::ref_seq from benchmark * [DOC] add CHANGELOG * Apply suggestions from code review * Apply suggestions from code review * Update CHANGELOG.md Co-authored-by: Enrico Seiler <[email protected]> Co-authored-by: marehr <[email protected]> Co-authored-by: Marcel <[email protected]> Co-authored-by: simonsasse <[email protected]> Co-authored-by: Lydia Buntrock <[email protected]>
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sam_file_output does not need the fields ref_seq, evalue, bit_score.
This commit remove those fields from the default-fields and ensures that custom fields don't contain those fields.
This commit also splits ::push_back and ::emplace_back into four versions to deprecate the usage of the old default-fields case.