Add TSV file support and a demo #2428
Conversation
There was a problem hiding this comment.
Hello there! If that is not quite the suprise 😄
So first of all thanks for your commitment to add a another file format. We are basically in a development freeze in favour of SeqAn3 but appreciate contributions. But I have some open requests for this. The most important thing is that I don't see any tests, which would be required before this can be added. The second thnig is that it feels more as it could be part of a text_io module which is a generic text file not associated with any particular file formats. Another format could be csv for example and this module would then be structured more like the seq_io.
| CTestTestfile.cmake | ||
| cmake_install.cmake | ||
| Makefile | ||
| .vscode |
There was a problem hiding this comment.
That looks like a fixup of in-source builds. Can you please remove this but keep the .vscode and make it a separate commit.
There was a problem hiding this comment.
I think that non of these should be changed, not even .vscode. If you need custom exclusion you can always add those to .git/info/exclude.
There was a problem hiding this comment.
well true, but .vscode is a common hidden directory for visual studio code which gains popularity. So I wouldn't mind but I have no strong feelings either.
| /*! | ||
| * @tag FileFormats#Tsv | ||
| * @headerfile <seqan/tsv_io.h> | ||
| * @brief Variant callinf format file. |
There was a problem hiding this comment.
| * @brief Variant callinf format file. | |
| * @brief Variant calling format file. |
Why is this bound to variant calling?
As far as I understand it merely reads in tab-separated text files.
Accordingly I would put this all into a text_io module, from which tsv is one supported format. Csv could be another. Similar to seq_io.
| /*! | ||
| * @class TsvRecord | ||
| * @implements FormattedFileHeaderConcept | ||
| * @headerfile <seqan/vcf_io.h> |
Hey! I needed to modify huge amounts of TSV files and as SeqAn is the one and only library to do this efficiently I wanted to contribute some code 😊