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leoislleoisl
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fix: now not erroring out when a non-ACGT base is in the query file
which is very common
1 parent edd5441 commit 4b582df

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7 files changed

+257
-37
lines changed

7 files changed

+257
-37
lines changed

‎.gitignore

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -11,3 +11,4 @@ python/docs/_generated
1111
__pycache__
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cobs*.tar
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cobs*.tar.gz
14+
!tests/data/non_acgt_test/index.cobs_classic

‎cobs/util/query.cpp

Lines changed: 34 additions & 34 deletions
Original file line numberDiff line numberDiff line change
@@ -140,44 +140,44 @@ void destroy_mmap(MMapHandle& handle)
140140
close_file(handle.fd);
141141
}
142142

143-
//! forward character map. A -> A, C -> C, G -> G, T -> T. rest maps to zero.
143+
//! forward character map. A -> A, C -> C, G -> G, T -> T. rest also maps to A to handle non-ACGT bases and not error out.
144144
static const char canonicalize_basepair_forward_map[256] = {
145-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
146-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
147-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
148-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
149-
0, 65, 0, 67, 0, 0, 0, 71, 0, 0, 0, 0, 0, 0, 0, 0,
150-
0, 0, 0, 0, 84, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
151-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
152-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
153-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
154-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
155-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
156-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
157-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
158-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
159-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
160-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
145+
65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65,
146+
65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65,
147+
65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65,
148+
65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65,
149+
65, 65, 65, 67, 65, 65, 65, 71, 65, 65, 65, 65, 65, 65, 65, 65,
150+
65, 65, 65, 65, 84, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65,
151+
65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65,
152+
65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65,
153+
65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65,
154+
65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65,
155+
65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65,
156+
65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65,
157+
65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65,
158+
65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65,
159+
65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65,
160+
65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65,
161161
};
162162

163-
//! reverse character map. A -> T, C -> G, G -> C, T -> A. rest maps to zero.
163+
//! reverse character map. A -> T, C -> G, G -> C, T -> A. rest also maps to T to handle non-ACGT bases and not error out.
164164
static const char canonicalize_basepair_reverse_map[256] = {
165-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
166-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
167-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
168-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
169-
0, 84, 0, 71, 0, 0, 0, 67, 0, 0, 0, 0, 0, 0, 0, 0,
170-
0, 0, 0, 0, 65, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
171-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
172-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
173-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
174-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
175-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
176-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
177-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
178-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
179-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
180-
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
165+
84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84,
166+
84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84,
167+
84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84,
168+
84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84,
169+
84, 84, 84, 71, 84, 84, 84, 67, 84, 84, 84, 84, 84, 84, 84, 84,
170+
84, 84, 84, 84, 65, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84,
171+
84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84,
172+
84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84,
173+
84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84,
174+
84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84,
175+
84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84,
176+
84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84,
177+
84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84,
178+
84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84,
179+
84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84,
180+
84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84,
181181
};
182182

183183
bool canonicalize_kmer(const char* input, char* output, uint64_t size)

‎tests/data/non_acgt_test/index.cobs_classic

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‎tests/data/non_acgt_test/test_1.fastq.gz

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‎tests/data/non_acgt_test/truth.out

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*ERR5069949.2151832 1
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genome 120
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genome 47
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‎tests/non_acgt_test.cpp

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1+
#include "test_util.hpp"
2+
#include <cobs/util/fs.hpp>
3+
#include <gtest/gtest.h>
4+
5+
namespace fs = cobs::fs;
6+
7+
static fs::path base_dir = "data/non_acgt_test";
8+
static fs::path work_dir = base_dir / "work";
9+
10+
class non_acgt_test : public ::testing::Test
11+
{
12+
protected:
13+
static void SetUpTestSuite() {
14+
cobs::error_code ec;
15+
fs::create_directories(work_dir, ec);
16+
}
17+
static void TearDownTestSuite() {
18+
cobs::error_code ec;
19+
fs::remove_all(work_dir, ec);
20+
}
21+
};
22+
23+
24+
TEST_F(non_acgt_test, non_acgt_test_main_test) {
25+
fs::path index_file{base_dir / "index.cobs_classic"};
26+
cobs::ClassicSearch s(index_file);
27+
fs::path query_file{base_dir / "test_1.fastq.gz"};
28+
auto query_out_filepath = work_dir / "query.out";
29+
std::ofstream query_out_fh(query_out_filepath.string());
30+
cobs::process_query(s, 0.80000000000000004, 0, "", query_file.string(), query_out_fh);
31+
query_out_fh.close();
32+
assert_equals_files_with_paths(
33+
base_dir / "truth.out",
34+
query_out_filepath);
35+
}

‎tests/util.cpp

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -50,13 +50,13 @@ TEST(util, kmer_canonicalize) {
5050

5151
// one kmer already canonical but containing invalid letters
5252
test_kmer("AGGAAAGTCTTTTACGCTGGGXXXAGAGTGA",
53-
"AGGAAAGTCTTTTACGCTGGG\0\0\0AGAGTGA", false);
53+
"AGGAAAGTCTTTTACGCTGGGAAAAGAGTGA", true);
5454
// one k-mer needing flipping containing invalid letters
5555
test_kmer("TGGAAAGTCTTTTACGCTGGGXXXAGAGTGA",
56-
"TCACTCT\0\0\0CCCAGCGTAAAAGACTTTCCA", false);
56+
"TCACTCTTTTCCCAGCGTAAAAGACTTTCCA", true);
5757
// one kmer containing the invalid letter at the center
5858
test_kmer("AAAAAAAAAAAAAAAXTTTTTTTTTTTTTTT",
59-
"AAAAAAAAAAAAAAA\0TTTTTTTTTTTTTTT", false);
59+
"AAAAAAAAAAAAAAAATTTTTTTTTTTTTTT", true);
6060
}
6161

6262
/******************************************************************************/

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