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Old 09-08-2011, 10:14 AM   #1
feederbing
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Default 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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Old 09-08-2011, 02:35 PM   #2
nilshomer
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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.
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Old 09-08-2011, 03:21 PM   #3
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Quote:
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!
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