faSplit -outDirDepth #18
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… current directory when running on 100k sequences. Don't use inputdir to find split files because they are in current directory which may not be inputdir.
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When running with a large number of sequences (which I realize is no longer the norm for you Rob, but some of us may need to when starting out), it's nice to use a temporary directory and faSplit's -outDirDepth=N option so that a large number of files aren't added in a single directory.
Also, inputdir was used as the location of the temporary files when concatenating, but faSplit creates them in the current directory (unless otherwise specified), so that would fail if inputdir were not the current directory.
If you approve of this, FYI I also plan to add the use of ${TMPDIR} if defined as the location of the temporary files.
Thanks!
Angie