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From 9c71f743217efb5728722fbe3eb11bf9a1efe66e Mon Sep 17 00:00:00 2001
From: Enrico Seiler <enrico.seiler@hotmail.de>
Date: Mon, 13 Jun 2022 16:46:56 +0200
Subject: [PATCH 05/12] [NOAPI] [DETAIL] Unused variables
---
test/snippet/alphabet/views/translate_usage.cpp | 15 ++++++++-------
test/snippet/alphabet/views/translate_usage.err | 7 +++++++
.../snippet/alphabet/views/trim_quality_dna5q.cpp | 11 ++++-------
.../snippet/alphabet/views/trim_quality_dna5q.err | 3 +++
.../alphabet/views/trim_quality_phred42.cpp | 13 +++++++++----
.../alphabet/views/trim_quality_phred42.err | 4 ++++
6 files changed, 35 insertions(+), 18 deletions(-)
create mode 100644 test/snippet/alphabet/views/translate_usage.err
create mode 100644 test/snippet/alphabet/views/trim_quality_dna5q.err
create mode 100644 test/snippet/alphabet/views/trim_quality_phred42.err
diff --git a/test/snippet/alphabet/views/translate_usage.cpp b/test/snippet/alphabet/views/translate_usage.cpp
index 9412a39ff..cfb82d4de 100644
--- a/test/snippet/alphabet/views/translate_usage.cpp
+++ b/test/snippet/alphabet/views/translate_usage.cpp
@@ -1,6 +1,7 @@
#include <seqan3/alphabet/nucleotide/dna5.hpp>
#include <seqan3/alphabet/views/complement.hpp>
#include <seqan3/alphabet/views/translate.hpp>
+#include <seqan3/core/debug_stream.hpp>
int main()
{
@@ -10,29 +11,29 @@ int main()
// default frame translation
auto v1 = vec | seqan3::views::translate;
- // == [[T,Y,V,R],[R,T,Y,V],[V,R,T],[Y,V,R,T],[T,Y,V,R],[R,T,Y]]
+ seqan3::debug_stream << v1 << '\n'; // [TYVR,RTYV,VRT,YVRT,TYVR,RTY]
// single frame translation
auto v2 = vec | seqan3::views::translate(seqan3::translation_frames::forward_frame0);
- // == [[T,Y,V,R]]
+ seqan3::debug_stream << v2 << '\n'; // [TYVR]
// reverse translation
auto v3 = vec | seqan3::views::translate(seqan3::translation_frames::forward_reverse0);
- // == [[T,Y,V,R],[Y,V,R,T]]
+ seqan3::debug_stream << v3 << '\n'; // [TYVR,YVRT]
// forward frames translation
auto v4 = vec | seqan3::views::translate(seqan3::translation_frames::forward_frames);
- // == [[T,Y,V,R],[R,T,Y,V],[V,R,T]]
+ seqan3::debug_stream << v4 << '\n'; // [TYVR,RTYV,VRT]
// six frame translation
auto v5 = vec | seqan3::views::translate(seqan3::translation_frames::six_frames);
- // == [[T,Y,V,R],[R,T,Y,V],[V,R,T],[Y,V,R,T],[T,Y,V,R],[R,T,Y]]
+ seqan3::debug_stream << v5 << '\n'; // [TYVR,RTYV,VRT,YVRT,TYVR,RTY]
// function syntax
auto v6 = seqan3::views::translate(vec, seqan3::translation_frames::forward_reverse0);
- // == [[T,Y,V,R],[Y,V,R,T]]
+ seqan3::debug_stream << v6 << '\n'; // [TYVR,YVRT]
// combinability
auto v7 = vec | seqan3::views::complement | seqan3::views::translate(seqan3::translation_frames::forward_reverse0);
- // == [[C,M,H,A],[M,H,A,C]]
+ seqan3::debug_stream << v7 << '\n'; // [CMHA,MHAC]
}
diff --git a/test/snippet/alphabet/views/translate_usage.err b/test/snippet/alphabet/views/translate_usage.err
new file mode 100644
index 000000000..b1e0a434e
--- /dev/null
+++ b/test/snippet/alphabet/views/translate_usage.err
@@ -0,0 +1,7 @@
+[TYVR,RTYV,VRT,YVRT,TYVR,RTY]
+[TYVR]
+[TYVR,YVRT]
+[TYVR,RTYV,VRT]
+[TYVR,RTYV,VRT,YVRT,TYVR,RTY]
+[TYVR,YVRT]
+[CMHA,MHAC]
diff --git a/test/snippet/alphabet/views/trim_quality_dna5q.cpp b/test/snippet/alphabet/views/trim_quality_dna5q.cpp
index 6795aedd3..be9bad4a5 100644
--- a/test/snippet/alphabet/views/trim_quality_dna5q.cpp
+++ b/test/snippet/alphabet/views/trim_quality_dna5q.cpp
@@ -6,6 +6,7 @@
#include <seqan3/alphabet/quality/phred42.hpp>
#include <seqan3/alphabet/views/to_char.hpp>
#include <seqan3/alphabet/views/trim_quality.hpp>
+#include <seqan3/core/debug_stream.hpp>
int main()
{
@@ -16,20 +17,16 @@ int main()
{'G'_dna5, '?'_phred42},
{'A'_dna5, '5'_phred42},
{'T'_dna5, '+'_phred42}};
- std::vector<seqan3::dna5q> cmp{{'A'_dna5, 'I'_phred42},
- {'G'_dna5, 'I'_phred42},
- {'G'_dna5, '?'_phred42},
- {'A'_dna5, '5'_phred42}};
// trim by phred_value
auto v1 = vec | seqan3::views::trim_quality(20u);
- assert(std::ranges::equal(v1, cmp));
+ seqan3::debug_stream << v1 << '\n'; // AGGA
// trim by quality character; in this case the nucleotide part of the character is irrelevant
auto v2 = vec | seqan3::views::trim_quality(seqan3::dna5q{'C'_dna5, '5'_phred42});
- assert(std::ranges::equal(v2, cmp));
+ seqan3::debug_stream << v2 << '\n'; // AGGA
// combinability
auto v3 = seqan3::views::trim_quality(vec, 20u) | seqan3::views::to_char;
- assert(std::ranges::equal(std::string{"AGGA"}, v3));
+ seqan3::debug_stream << v3 << '\n'; // AGGA
}
diff --git a/test/snippet/alphabet/views/trim_quality_dna5q.err b/test/snippet/alphabet/views/trim_quality_dna5q.err
new file mode 100644
index 000000000..b6f022a15
--- /dev/null
+++ b/test/snippet/alphabet/views/trim_quality_dna5q.err
@@ -0,0 +1,3 @@
+AGGA
+AGGA
+AGGA
diff --git a/test/snippet/alphabet/views/trim_quality_phred42.cpp b/test/snippet/alphabet/views/trim_quality_phred42.cpp
index dad15b221..702578f6e 100644
--- a/test/snippet/alphabet/views/trim_quality_phred42.cpp
+++ b/test/snippet/alphabet/views/trim_quality_phred42.cpp
@@ -4,6 +4,7 @@
#include <seqan3/alphabet/quality/phred42.hpp>
#include <seqan3/alphabet/views/to_char.hpp>
#include <seqan3/alphabet/views/trim_quality.hpp>
+#include <seqan3/core/debug_stream.hpp>
using namespace seqan3::literals;
@@ -12,14 +13,18 @@ int main()
std::vector<seqan3::phred42> vec{"II?5+"_phred42};
// trim by phred_value
- auto v1 = vec | seqan3::views::trim_quality(20u); // == ['I','I','?','5']
+ auto v1 = vec | seqan3::views::trim_quality(20u);
+ seqan3::debug_stream << v1 << '\n'; // II?5
// trim by quality character
- auto v2 = vec | seqan3::views::trim_quality('I'_phred42); // == ['I','I']
+ auto v2 = vec | seqan3::views::trim_quality('I'_phred42);
+ seqan3::debug_stream << v2 << '\n'; // II
// function syntax
- auto v3 = seqan3::views::trim_quality(vec, '5'_phred42); // == ['I','I','?','5']
+ auto v3 = seqan3::views::trim_quality(vec, '5'_phred42);
+ seqan3::debug_stream << v3 << '\n'; // II?5
// combinability
- auto v4 = seqan3::views::trim_quality(vec, 20u) | seqan3::views::to_char; // == "II?5"
+ auto v4 = seqan3::views::trim_quality(vec, 20u) | seqan3::views::to_char;
+ seqan3::debug_stream << v4 << '\n'; // II?5
}
diff --git a/test/snippet/alphabet/views/trim_quality_phred42.err b/test/snippet/alphabet/views/trim_quality_phred42.err
new file mode 100644
index 000000000..d530c3716
--- /dev/null
+++ b/test/snippet/alphabet/views/trim_quality_phred42.err
@@ -0,0 +1,4 @@
+II?5
+II
+II?5
+II?5
--
2.34.1
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