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From e59dbf474f3bc714a6ef53e101bc4f0e65a1bf82 Mon Sep 17 00:00:00 2001
From: Simon Gene Gottlieb <simon@gottliebtfreitag.de>
Date: Tue, 1 Apr 2025 15:24:33 +0200
Subject: [PATCH 9/9] [FIX] include alignment_printer in debug_stream
---
.../pairwise_alignment_solution_4.err | 6 +++++-
.../pairwise_alignment_solution_5.err | 6 +++++-
.../cigar_conversion/alignment_from_cigar.err | 6 +++++-
.../alignment_from_cigar_io.err | 18 +++++++++++++++---
.../align_cfg_output_examples.err | 18 +++++++++++++++---
5 files changed, 45 insertions(+), 9 deletions(-)
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 1889cdb7a..4aa696a7e 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 1889cdb7a..4aa696a7e 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/test/snippet/alignment/cigar_conversion/alignment_from_cigar.err b/test/snippet/alignment/cigar_conversion/alignment_from_cigar.err
index 269fcf4f8..c771bf5a9 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 65e809957..43d4207db 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 43207860d..9dfe1222c 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
+}
--
2.49.0
|
