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
$ 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:
The corrected code is:
I have placed a patch file on my web site at
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.)