Closed smehringer closed 1 year ago
This error was introduced by https://github.com/seqan/seqan3/pull/3104
when I read FASTA file with alphabt = char, newlines are in my string.
The following test fails
struct char_traits : public seqan3::sequence_file_input_default_traits_dna { using sequence_alphabet = char; using sequence_legal_alphabet = char; }; using sequence_file_type = seqan3::sequence_file_input<char_traits, seqan3::fields<seqan3::field::id, seqan3::field::seq>, seqan3::type_list<seqan3::format_fasta>>; TEST_F(read, whitespace_in_seq_char_alphabet) { std::string input{">ID1\n" "ACGTTTT\n\nTTTTTTTTTTT\n" "\n" ">ID2\n" "ACGTTTT\t\tTTTTTTTTTTT\t\nTTTTTTTTTTT\vTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\rTTTTTTTTTTTTTTTTT\n" ">ID3 lala\n" "ACGT\fTTA\n"}; std::stringstream istream{input}; sequence_file_type fin{istream, seqan3::format_fasta{}}; auto it = fin.begin(); for (unsigned i = 0; i < 3; ++i, ++it) { EXPECT_EQ((*it).id(), ids[i]); EXPECT_RANGE_EQ((*it).sequence(), seqs[i] | seqan3::views::to_char); } }
with (only showing the error for i = 0)
i = 0
Expected equality of these values: (*it).sequence() Which is: ACGTTTT TTTTTTTTTTT seqs[i] | seqan3::views::to_char Which is: ACGTTTTTTTTTTTTTTT
Test passes. No newlines in my sequence.
Copy into fasta test and run.
- Operating system: Linux - SeqAn version: current master - Compiler: GCC-10.4
No response
Does this problem persist on the current master?
Is there an existing issue for this?
Current Behavior
This error was introduced by https://github.com/seqan/seqan3/pull/3104
when I read FASTA file with alphabt = char, newlines are in my string.
The following test fails
with (only showing the error for
i = 0
)Expected Behavior
Test passes. No newlines in my sequence.
Steps To Reproduce
Copy into fasta test and run.
Environment
Anything else?
No response