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.rgdict and .seqdict files are not placed in the adam directory #945

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jpdna opened this Issue Feb 16, 2016 · 3 comments

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jpdna commented Feb 16, 2016

This may not be a bug, but I wanted to check that it is intentional that the .adam.rgdict and .adam.seqdict when creating .adam files with transform appear in the filesystem directory structure as siblings to the parquet .adam directory.
If these cannot go in the parquet .adam directory, could they at instead go into a .adam.dicts directory to keep the dir structure a little cleaner?

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heuermh Feb 17, 2016

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Note there are also .{name}.adam.rgdict.crc and .{name}.adam.seqdict.crc files.

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heuermh commented Feb 17, 2016

Note there are also .{name}.adam.rgdict.crc and .{name}.adam.seqdict.crc files.

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heuermh Mar 22, 2016

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The more I think about this, the more I think they should go in the .adam directory. I'm always bothered by other tools' handling of extra files (e.g. bowtie indices, picard sequence dictionaries, etc.), sometimes using command line arguments, sometimes using file base names, sometimes with certain file extensions, sometimes not.

Can we just hide these in the .adam directory and never have the user refer to them?

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heuermh commented Mar 22, 2016

The more I think about this, the more I think they should go in the .adam directory. I'm always bothered by other tools' handling of extra files (e.g. bowtie indices, picard sequence dictionaries, etc.), sometimes using command line arguments, sometimes using file base names, sometimes with certain file extensions, sometimes not.

Can we just hide these in the .adam directory and never have the user refer to them?

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heuermh Mar 24, 2016

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Bummer about all the linked dead commits, guess if you add fixes ... to the commit message, it stays on the linked issue page even if the commit has been rebased and force pushed out of existence.

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heuermh commented Mar 24, 2016

Bummer about all the linked dead commits, guess if you add fixes ... to the commit message, it stays on the linked issue page even if the commit has been rebased and force pushed out of existence.

@fnothaft fnothaft closed this in #978 Mar 29, 2016

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