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SSAHA bug fix

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  • Conrad Halling
    SSAHA Users, There is a minor bug in SSAHA that results in no alignments being produced when you re working with large subject files while using a short word
    Message 1 of 1 , Jan 26, 2006
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      SSAHA Users,

      There is a minor bug in SSAHA that results in no alignments being
      produced when you're working with large subject files while using a
      short word length. For example, searching human chromosome 2, which has
      a length of 243,000,000 bp, using a word length of 6 (-wl 6), gives the
      following output:

      $ ssaha alu1.fa chr2.fa -sl 1 -wl 5 -pf -mp 25 -da 0
      [... output omitted ...]
      Info: would expect 57984.2 hits per word for a random database of this size.
      Info: will ignore hits on words that occur more than -2147483648 times
      in the database.

      This bug occurred on line 785 of SSAHAMain.cpp. The original code was:

      queryParams.maxStore=1+(int)(expectedNumHits*queryParams.maxStore);

      The corrected code is:

      queryParams.maxStore=(int)(expectedNumHits*queryParams.maxStore);

      I have placed a patch file on my web site at
      http://www.bifx.org/SSAHA/index.html along with instructions on how to
      apply the patch. (The patch contains my earlier corrections to SSAHA
      that allow you to compile SSAHA with GCC 4.0.x and that allow you to run
      SSAHA on a PowerPC-based Mac OS X computer.)

      -- Conrad

      --
      Conrad Halling
      conrad.halling@...
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