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  • feederbing
    replied
    Originally posted by nilshomer View Post
    The index is compressed (with gzip) on disk, and so the index size reported is the size in memory. Use "bheader" to get info about the index.
    T h a n k s!

    Leave a comment:


  • nilshomer
    replied
    The index is compressed (with gzip) on disk, and so the index size reported is the size in memory. Use "bheader" to get info about the index.

    Leave a comment:


  • feederbing
    started a topic Any way to validate BFAST index file?

    Any way to validate BFAST index file?

    Continuing my experiments with bfasta (see http://seqanswers.com/forums/showthr...0855#post50855 ), I've built an index for a specific mask. I am getting conflicting file sizes for the index file, though. My command to build the index is
    time bfast index -A 0 -f reference.fa \
    -i 1 -m 10011110101111101111101101101 -w 14 -R

    And among other info, the program reports "Index size is 8.007GB". However, a ls of the directory reports the file size as 6.5G. So I don't know if the entire file has been written to disk, or if b=fast is misreporting the size.

    Is there any tool that will validate whether my index file is complete and correct?

    Thanks

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