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statgen / ruth

Robust Unified Hardy-Weinberg Equilibrium Test
Apache License 2.0
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Chunking? #9

Open jjfarrell opened 1 year ago

jjfarrell commented 1 year ago

What does chunking do? Why would you use that parameter?

I tried running it to see, but I get this message. WARNING [2023/06/28 22:33:06] - [W:/share/pkg.7/ruth/git778d784/src/ruth/bcf_filtered_reader.cpp:78 void BCFFilteredReader::init_params()] ref_file_name or interval_file_name is used but will be ignored because chunking is not necessary. Use -CHR- in the filename if you intended chunking the file

Is this in the input or output file that needs the 'CHR"? Is chunking used to split it by chromosome or some standard chr length?

An example would be helpful.

hyunminkang commented 1 year ago

Chunking was intended to support a series of BCF following specific naming convention, in the case that the user wants to split BCF file into multiple pieces.

However, we no longer support this chunking system. So please do not use the chunking option.