diff --git a/doc/tutorial/08_pairwise_alignment/pairwise_alignment_solution_4.err b/doc/tutorial/08_pairwise_alignment/pairwise_alignment_solution_4.err index 1889cdb7a6..4aa696a7e0 100644 --- a/doc/tutorial/08_pairwise_alignment/pairwise_alignment_solution_4.err +++ b/doc/tutorial/08_pairwise_alignment/pairwise_alignment_solution_4.err @@ -2,4 +2,8 @@ Score: 62 Begin: (4,0) End: (34,31) Alignment: -(GTACGGAC-T-AGCTACAACATTACGGACTAC,GGAC-GACATGACGTACGACTTTACGTACGAC) + 0 . : . : . : + GTACGGAC-T-AGCTACAACATTACGGACTAC + | || ||| | | ||| || ||||| || || + GGAC-GACATGACGTACGACTTTACGTACGAC + diff --git a/doc/tutorial/08_pairwise_alignment/pairwise_alignment_solution_5.err b/doc/tutorial/08_pairwise_alignment/pairwise_alignment_solution_5.err index 1889cdb7a6..4aa696a7e0 100644 --- a/doc/tutorial/08_pairwise_alignment/pairwise_alignment_solution_5.err +++ b/doc/tutorial/08_pairwise_alignment/pairwise_alignment_solution_5.err @@ -2,4 +2,8 @@ Score: 62 Begin: (4,0) End: (34,31) Alignment: -(GTACGGAC-T-AGCTACAACATTACGGACTAC,GGAC-GACATGACGTACGACTTTACGTACGAC) + 0 . : . : . : + GTACGGAC-T-AGCTACAACATTACGGACTAC + | || ||| | | ||| || ||||| || || + GGAC-GACATGACGTACGACTTTACGTACGAC + diff --git a/include/seqan3/core/debug_stream.hpp b/include/seqan3/core/debug_stream.hpp index 1b91930391..f4e2a680f5 100644 --- a/include/seqan3/core/debug_stream.hpp +++ b/include/seqan3/core/debug_stream.hpp @@ -11,6 +11,7 @@ #include +#include #include #include diff --git a/test/snippet/alignment/cigar_conversion/alignment_from_cigar.err b/test/snippet/alignment/cigar_conversion/alignment_from_cigar.err index 269fcf4f88..c771bf5a93 100644 --- a/test/snippet/alignment/cigar_conversion/alignment_from_cigar.err +++ b/test/snippet/alignment/cigar_conversion/alignment_from_cigar.err @@ -1 +1,5 @@ -(ACTGA,AC-GA) + 0 . + ACTGA + || || + AC-GA + diff --git a/test/snippet/alignment/cigar_conversion/alignment_from_cigar_io.err b/test/snippet/alignment/cigar_conversion/alignment_from_cigar_io.err index 65e8099578..43d4207db8 100644 --- a/test/snippet/alignment/cigar_conversion/alignment_from_cigar_io.err +++ b/test/snippet/alignment/cigar_conversion/alignment_from_cigar_io.err @@ -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 + diff --git a/test/snippet/alignment/configuration/align_cfg_output_examples.err b/test/snippet/alignment/configuration/align_cfg_output_examples.err index 43207860d0..9dfe1222c8 100644 --- a/test/snippet/alignment/configuration/align_cfg_output_examples.err +++ b/test/snippet/alignment/configuration/align_cfg_output_examples.err @@ -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 +} diff --git a/test/unit/utility/views/chunk_test.cpp b/test/unit/utility/views/chunk_test.cpp index 2e6def8d40..145151ab95 100644 --- a/test/unit/utility/views/chunk_test.cpp +++ b/test/unit/utility/views/chunk_test.cpp @@ -9,7 +9,6 @@ #include #include -#include #include #include #include