Add a skeleton VCF parser which can print variants in VCF output. #46
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Irallia
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eaasna
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eaasna
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Jan 31, 2021
| @@ -0,0 +1,193 @@ | |||
| #include <seqan3/io/stream/concept.hpp> | |||
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What's the connection to the seqan3 VCF parser? Will you also be using it?
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Hi! So at the moment, seqan3 doesn't have a VCF parser implemented. So the one I'm implementing here will be used as a sort of framework for the future seqan3 implementation!
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I see, thanks for the explanation!
Irallia
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| /*! \brief Set the file format for this VCF file header. | ||
| * | ||
| * \param fileformati The input fileformat. | ||
| */ | ||
| void set_fileformat(std::string fileformati) | ||
| { | ||
| fileformat = fileformati; | ||
| } |
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Just an idea, so it doesn't look like a typo:
Suggested change
| /*! \brief Set the file format for this VCF file header. | |
| * | |
| * \param fileformati The input fileformat. | |
| */ | |
| void set_fileformat(std::string fileformati) | |
| { | |
| fileformat = fileformati; | |
| } | |
| /*! \brief Set the file format for this VCF file header. | |
| * | |
| * \param fileformat_i The input fileformat. | |
| */ | |
| void set_fileformat(std::string fileformat_i) | |
| { | |
| fileformat = fileformat_i; | |
| } |
| #include <seqan3/io/stream/concept.hpp> | ||
| #include <fstream> | ||
| #include <map> | ||
|
|
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I would add a short description like
/*
* We're using the The Variant Call Format (VCF) Specification: VCFv4.3 and BCFv2.2
* https://samtools.github.io/hts-specs/VCFv4.3.pdf
*/| #include <fstream> | ||
| #include <map> | ||
|
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||
| class info_entry |
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And maybe something like this for the info_enty class:
/*
* An Info field looks like:
* ##INFO=<ID=ID,Number=number,Type=type,Description="description",Source="source",Version="version">
* https://samtools.github.io/hts-specs/VCFv4.3.pdf (1.4.2 Information field format)
*/
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Resolves #9 and resolves #10.
Here I introduce a skeleton VCF parser to address issue #29. It doesn't really do any checking to make sure values are valid, but it does provide a template for information regarding variants to be stored in a VCF format-friendly way.
Some things up for discussion:
variant_headerandvariant_recordare currently empty, because I figured all of the information is not always known on construction. But maybe it makes sense to change this?