ReadSeq large sequence bug
francis at monod.Biol.McGill.CA
Sun Apr 25 08:49:06 EST 1993
gilbertd at sunflower.bio.indiana.edu (Don Gilbert) writes:
>There is a bug in the current release of readseq (dated 1Feb93)
>which causes it to abort when fed sequences larger than a certain
>size, at least when compiled with certain compilers. If you
>feed a sequence of around 5000 base pairs or larger to readseq,
>and it aborts (maybe with the message "Segmentation fault") then
>you have found the bug.
>Here is a temporary correction for that bug.
>In the file ureadseq.c, change near top:
>#define kStartLength 500
>#define kStartLength 500000 /* 20Apr93 temp. bug fix */
> /* set this value higher than max seq size expected */
>then recompile it, and readseq will work on large sequences.
>(tobacco chlorop. gene acc#Z00044 with 155844 bp for example)
>But this isn't a definative bug fix. It looks like the
>memory management code for calloc/malloc/realloc is failing
>where it shouldn't. I will have to look at it more.
well it works fine on 50-60 k files, but it did core dump with
the yeast chromosome III file (315k) :-)
(on a sparc2, SunOS 4.1.2, compilled with gcc (I forget the version #)
but this is fine (for now anyways!)
thank you very much Don,
| B.F. Francis Ouellette * francis at monod.biol.mcgill.ca *
| "Je cherche a` comprendre" Jacques Monod
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