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fix: include alignment printer in debug_stream.h #3355

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Merged
eseiler merged 3 commits into from
Apr 1, 2025
Merged

fix: include alignment printer in debug_stream.h #3355

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f40e497
fix: include alignment printer in debug_stream.h
SGSSGene Apr 1, 2025
3bd411e
fix: remove unused include
SGSSGene Apr 1, 2025
e7d7999
fix: adjust alignment printing cigar string
SGSSGene Apr 1, 2025
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6 changes: 5 additions & 1 deletion doc/tutorial/08_pairwise_alignment/pairwise_alignment_solution_4.err
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Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,8 @@ Score: 62
Begin: (4,0)
End: (34,31)
Alignment:
(GTACGGAC-T-AGCTACAACATTACGGACTAC,GGAC-GACATGACGTACGACTTTACGTACGAC)
0 . : . : . :
GTACGGAC-T-AGCTACAACATTACGGACTAC
| || ||| | | ||| || ||||| || ||
GGAC-GACATGACGTACGACTTTACGTACGAC

6 changes: 5 additions & 1 deletion doc/tutorial/08_pairwise_alignment/pairwise_alignment_solution_5.err
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Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,8 @@ Score: 62
Begin: (4,0)
End: (34,31)
Alignment:
(GTACGGAC-T-AGCTACAACATTACGGACTAC,GGAC-GACATGACGTACGACTTTACGTACGAC)
0 . : . : . :
GTACGGAC-T-AGCTACAACATTACGGACTAC
| || ||| | | ||| || ||||| || ||
GGAC-GACATGACGTACGACTTTACGTACGAC

1 change: 1 addition & 0 deletions include/seqan3/core/debug_stream.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@

#include <iostream>

#include <seqan3/alignment/aligned_sequence/debug_stream_alignment.hpp>
#include <seqan3/alphabet/detail/debug_stream_alphabet.hpp>
#include <seqan3/core/debug_stream/all.hpp>

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6 changes: 5 additions & 1 deletion test/snippet/alignment/cigar_conversion/alignment_from_cigar.err
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Original file line number Diff line number Diff line change
@@ -1 +1,5 @@
(ACTGA,AC-GA)
0 .
ACTGA
|| ||
AC-GA

18 changes: 15 additions & 3 deletions test/snippet/alignment/cigar_conversion/alignment_from_cigar_io.err
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Original file line number Diff line number Diff line change
@@ -1,3 +1,15 @@
(ACT-,C-GT)
(CTGATCGAG,AGGCTGN-A)
(T-G-A-TC,G-AGTA-T)
0
ACT-

C-GT

0 .
CTGATCGAG
| |
AGGCTGN-A

0 .
T-G-A-TC
|
G-AGTA-T

18 changes: 15 additions & 3 deletions test/snippet/alignment/configuration/align_cfg_output_examples.err
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Original file line number Diff line number Diff line change
@@ -1,10 +1,22 @@
{score: -4}
{
alignment:
(ACGTA-G-C-,A-GTACGACG)}
0 . :
ACGTA-G-C-
| ||| | |
A-GTACGACG
}
{score: -4,
alignment:
(ACGTA-G-C-,A-GTACGACG)}
0 . :
ACGTA-G-C-
| ||| | |
A-GTACGACG
}
{sequence1 id: 0, sequence2 id: 0, score: -4, begin: (0,0), end: (7,9),
alignment:
(ACGTA-G-C-,A-GTACGACG)}
0 . :
ACGTA-G-C-
| ||| | |
A-GTACGACG
}
1 change: 0 additions & 1 deletion test/unit/utility/views/chunk_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,6 @@
#include <ranges>
#include <vector>

#include <seqan3/core/debug_stream.hpp>
#include <seqan3/test/expect_range_eq.hpp>
#include <seqan3/utility/views/chunk.hpp>
#include <seqan3/utility/views/repeat.hpp>
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