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vdauwera avatar vdauwera commented on July 17, 2024

@nh13 Do you have a pointer to where the list lives by any chance?

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vdauwera avatar vdauwera commented on July 17, 2024

Well, found out two things.

  1. This is defined in htsjdk's ReferenceSequenceFileFactory.java, not Picard itself.
  2. The .fna extension is included in there, and accordingly, the latest version of Picard happily creates a dict file for a reference provided with .fna extension.

So it looks like there's nothing to do.

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vdauwera avatar vdauwera commented on July 17, 2024

Actually, funny thing -- while .fna (which is what was originally requested) is in there, .fsa is not, nor is .fas, which is another common one I remember from bygone days. We also don't include .seq, which is listed on the wikipedia page referred to in the original request.

uploads/547b19ef-5c42-4fbb-a7a2-cf8885bf9c2b/Screenshot 2015-04-27 01.09.59.png

So, how far we want to go to accommodate the wildtype fastas out there?

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nh13 avatar nh13 commented on July 17, 2024

No need to overgeneralize unless users want it.

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