22 EST 1993
Article: 2195 of bionet.software
From: gilbertd at sunflower.bio.indiana.edu (Don Gilbert)
Subject: ReadSeq large sequence bug
Message-ID: <C5sF5H.Lvq at usenet.ucs.indiana.edu>
Sender: news at usenet.ucs.indiana.edu (USENET News System)
Organization: Biology, Indiana University - Bloomington
Date: Tue, 20 Apr 1993 15:03:15 GMT
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.
Don Gilbert gilbert at bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405