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Trim ID after first whitespace #112

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merged 1 commit into from
Sep 17, 2024
Merged

Trim ID after first whitespace #112

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2 changes: 2 additions & 0 deletions README.md
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Expand Up @@ -47,6 +47,8 @@
-->
[4]: https://codecov.io/gh/eaasna/valik

The FASTA identifiers are trimmed after the first whitespace.

## Quick run: split and search single reference sequence
`valik split test/data/split/single_reference.fasta --ref-meta reference_metadata.txt --seg-meta segment_metadata.txt --bins 4`

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8 changes: 3 additions & 5 deletions include/valik/split/metadata.hpp
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Expand Up @@ -13,6 +13,7 @@
#include <iostream>
#include <fstream>
#include <ranges>
#include <sstream>

#include <cereal/archives/binary.hpp>
#include <cereal/types/vector.hpp>
Expand All @@ -30,12 +31,9 @@ void trim_fasta_id(id_t & id)
auto first_valid = id.find_first_not_of(whitespace);
if (first_valid == std::string::npos)
throw std::runtime_error{"Sequence name can not be empty."};
id.erase(0, first_valid);

auto last_valid = id.find_last_not_of(whitespace);
if (last_valid == std::string::npos)
throw std::runtime_error{"Sequence name can not be empty."};
id.erase(last_valid + 1);
std::istringstream iss(id);
iss >> id;
}

/**
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