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[MISC] deprecate seqan3::alignment_file* entities #2459
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Codecov Report
@@ Coverage Diff @@
## master #2459 +/- ##
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Coverage 98.30% 98.30%
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Files 267 267
Lines 11063 11063
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Hits 10875 10875
Misses 188 188
Continue to review full report at Codecov.
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#include <seqan3/io/alignment_file/format_bam.hpp> | ||
#include <seqan3/io/alignment_file/format_sam.hpp> | ||
#include <seqan3/io/alignment_file/header.hpp> | ||
#include <seqan3/io/alignment_file/input.hpp> | ||
#include <seqan3/io/alignment_file/input_format_concept.hpp> | ||
#include <seqan3/io/alignment_file/input_options.hpp> | ||
#include <seqan3/io/alignment_file/output.hpp> | ||
#include <seqan3/io/alignment_file/output_format_concept.hpp> | ||
#include <seqan3/io/alignment_file/output_options.hpp> | ||
#include <seqan3/io/alignment_file/sam_tag_dictionary.hpp> |
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Are these includes still needed after #include <seqan3/io/sam_file/all.hpp>
?
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all.hpp
won't completely work, because some headers like #include <seqan3/io/alignment_file/input.hpp>
define the deprecated seqan3::alignment_file_input
.
So to be safe I just used the old include list without changing anything.
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Does that mean there will be 11 deprecation warnings when including seqan3/io/alignment_file/all.hpp
? 😁
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yeah, xD
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alignment_file_output_format
and alignment_file_input_format
do not show up in the documentation.
If you want to have a look, go ahead, otherwise you can merge
#include <seqan3/io/alignment_file/format_bam.hpp> | ||
#include <seqan3/io/alignment_file/format_sam.hpp> | ||
#include <seqan3/io/alignment_file/header.hpp> | ||
#include <seqan3/io/alignment_file/input.hpp> | ||
#include <seqan3/io/alignment_file/input_format_concept.hpp> | ||
#include <seqan3/io/alignment_file/input_options.hpp> | ||
#include <seqan3/io/alignment_file/output.hpp> | ||
#include <seqan3/io/alignment_file/output_format_concept.hpp> | ||
#include <seqan3/io/alignment_file/output_options.hpp> | ||
#include <seqan3/io/alignment_file/sam_tag_dictionary.hpp> |
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Does that mean there will be 11 deprecation warnings when including seqan3/io/alignment_file/all.hpp
? 😁
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duplicate post due to server error
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Part of seqan/product_backlog#290